From 3b665b094ccd08440f6996f47285351ea4a74f66 Mon Sep 17 00:00:00 2001 From: Brett Viren Date: Tue, 20 Jul 2021 10:31:47 -0400 Subject: [PATCH 01/15] Snapshot of adding multithreaded wct --- README.org | 2 +- cfg/main-depos-sim-adc.jsonnet | 2 +- cfg/toyzero.jsonnet | 20 +++++++++++--------- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/README.org b/README.org index 2dd8c98..9f812a9 100644 --- a/README.org +++ b/README.org @@ -3,7 +3,7 @@ #+setupfile: https://ls4gan.github.io/other/setup-page.org #+options: toc:t -The toyzero package provides first steps toward [[https://ls4gan.github.io/][LS4GAN]]. +The toyzero package provides first steps toward [[https://ls4gan.github.io/][LS4GAN]]. See also [[file:next-steps.org]] * Goals :PROPERTIES: diff --git a/cfg/main-depos-sim-adc.jsonnet b/cfg/main-depos-sim-adc.jsonnet index 6aceacb..96b83d3 100644 --- a/cfg/main-depos-sim-adc.jsonnet +++ b/cfg/main-depos-sim-adc.jsonnet @@ -10,7 +10,7 @@ // -A input=depos.npz -A output=frames.npz \ // -A wires=wires-geometry.json.bz2 \ // -A resps=field-response.json.bz2 \ -// -A noise="yes" \ +// -A noisef=/path/to/noise/model/file \ // -c main-depos-sim-adc.jsonnet // // The 'noise' TLA is optional and defaults to "no". diff --git a/cfg/toyzero.jsonnet b/cfg/toyzero.jsonnet index ca3721a..bab57f6 100644 --- a/cfg/toyzero.jsonnet +++ b/cfg/toyzero.jsonnet @@ -111,7 +111,9 @@ local pg = import "pgraph.jsonnet"; // The vol, daq, adc, lar likely comes from params. // The noisef should be a file name. // fixme: probably should be broken up... - apasim(anode, pirs, vol, daq, adc, lar, noisef=null, rnd=$.random()) : { + apasim(anode, pirs, vol, daq, adc, lar, noisef=null, tier='adc', rnd=$.random()) : { + + local tagbase = if tier == 'adc' then 'orig' else 'volt', local apaid = anode.data.ident, @@ -150,7 +152,7 @@ local pg = import "pgraph.jsonnet"; name: 'Digitizer%d' % apaid, data : adc { anode: wc.tn(anode), - frame_tag: "orig%d"%apaid, + frame_tag: "%s%d"%[tagbase, apaid], } }, nin=1, nout=1, uses=[anode]), @@ -184,7 +186,7 @@ local pg = import "pgraph.jsonnet"; local mid = if std.type(noisef) == "null" then [] else [noise], - local end = [digitizer], + local end = if tier == 'adc' then [digitizer] else [], pipeline: pg.pipeline(beg + mid + end), }.pipeline, @@ -192,12 +194,12 @@ local pg = import "pgraph.jsonnet"; local plugins = [ "WireCellSio", "WireCellAux", "WireCellGen", "WireCellSigProc", - "WireCellApps", "WireCellPgraph"], + "WireCellApps", "WireCellPgraph", "WireCellTbb"], - main(graph) :: { - local app = { - type: 'Pgrapher', + main(graph, app) :: { + local appcfg = { + type: app, data: { edges: pg.edges(graph) }, @@ -206,9 +208,9 @@ local pg = import "pgraph.jsonnet"; type: "wire-cell", data: { plugins: plugins, - apps: ["Pgrapher"], + apps: [appcfg.type] } }, - seq: [cmdline] + pg.uses(graph) + [app], + seq: [cmdline] + pg.uses(graph) + [appcfg], }.seq } From 834129d5a42c56794a84bf2e0f93438eec488ff7 Mon Sep 17 00:00:00 2001 From: Brett Viren Date: Wed, 21 Jul 2021 15:07:00 -0400 Subject: [PATCH 02/15] Factor config further and start longer sigproc chain --- cfg/main-depos-sigproc.jsonnet | 71 +++++++++++++ cfg/main-depos-sim-adc.jsonnet | 21 ++-- cfg/nf.jsonnet | 152 +++++++++++++++++++++++++++ cfg/sp.jsonnet | 85 +++++++++++++++ cfg/toyzero.jsonnet | 184 +++++++++++++++++++-------------- 5 files changed, 424 insertions(+), 89 deletions(-) create mode 100644 cfg/main-depos-sigproc.jsonnet create mode 100644 cfg/nf.jsonnet create mode 100644 cfg/sp.jsonnet diff --git a/cfg/main-depos-sigproc.jsonnet b/cfg/main-depos-sigproc.jsonnet new file mode 100644 index 0000000..9edb6e2 --- /dev/null +++ b/cfg/main-depos-sigproc.jsonnet @@ -0,0 +1,71 @@ +// This is a main wire-cell configuration file. +// +// It implements the chain: +// (depos)->sim(signal,noise)->sigproc->(signals) +// +// It takes a number of top-level-arguments (TLA). +// +// Run like +// +// wire-cell \ +// -A input=depos.npz -A output=frames.npz \ +// -A wires=wires-geometry.json.bz2 \ +// -A resps=field-response.json.bz2 \ +// -A noisef=/path/to/noise/model/file \ +// -A app=[Pgrapher|TbbFlow] \ +// -c main-depos-sim-adc.jsonnet +// +// The 'noisef' TLA is optional and specifies a noise model. If not +// given, only signal is simulated. + +local wc = import "wirecell.jsonnet"; +local pg = import "pgraph.jsonnet"; + +local tz = import "toyzero.jsonnet"; +local io = import "ioutils.jsonnet"; +local nf = import "nf.jsonnet"; +local sp = import "sp.jsonnet"; + +function(input, output, wires, resps, noisef=null, app='Pgrapher') +local seeds = [0,1,2,3,4]; // maybe let CLI set? +local depos = io.npz_source_depo("depos", input); + +local params = import "pgrapher/experiment/pdsp/simparams.jsonnet"; +local spfilt = import "pgrapher/experiment/pdsp/sp-filters.jsonnet"; + +local wireobj = tz.wire_file(wires); +local anodes = tz.anodes(wireobj, params.det.volumes); + +local apaids = std.range(0, std.length(anodes)-1); + +local robjs = tz.responses(resps, params.elec, params.daq); + +local random = tz.random(seeds); + +local drifter = tz.drifter(params.det.volumes, params.lar, random); +local bagger = tz.bagger(params.daq); + +local sim(n) = + tz.sim(anodes[n], robjs.pirs, + params.daq, params.adc, params.lar, + noisef, 'adc', random); + +local adcpermv = tz.adcpermv(params.adc); +local nfsp(n) = + pg.pipeline([ + nf(anodes[n], robjs.fr, params.daq.nticks, params.daq.tick), + sp(anodes[n], robjs.fr, robjs.er, spfilt, adcpermv)]); + +local oneapa(n) = pg.pipeline([sim(n), nfsp(n)]); + +local pipes = [oneapa(n) for n in apaids]; + +local frame_tags = ["gaus%d"%n for n in apaids]; +local frames = io.frame_save_npz("frames", output, + digitize = false, tags=frame_tags); +local dump = io.frame_sink(); + +local body = pg.fan.pipe('DepoSetFanout', pipes, 'FrameFanin'); +local full = pg.pipeline([depos, drifter, bagger, body, frames, dump]); +tz.main(full, app) + diff --git a/cfg/main-depos-sim-adc.jsonnet b/cfg/main-depos-sim-adc.jsonnet index 96b83d3..63b09f6 100644 --- a/cfg/main-depos-sim-adc.jsonnet +++ b/cfg/main-depos-sim-adc.jsonnet @@ -21,36 +21,35 @@ local pg = import "pgraph.jsonnet"; local tz = import "toyzero.jsonnet"; local io = import "ioutils.jsonnet"; -function(input, output, wires, resps, noisef=null) +function(input, output, wires, resps, noisef=null, app='Pgrapher') local seeds = [0,1,2,3,4]; // maybe let CLI set? local depos = io.npz_source_depo("depos", input); -local params = tz.protodune_params; +local params = import "pgrapher/experiment/pdsp/simparams.jsonnet"; local wireobj = tz.wire_file(wires); local anodes = tz.anodes(wireobj, params.det.volumes); local apaids = std.range(0, std.length(anodes)-1); -local pirs = tz.pirs(resps, params.daq, params.elec); +local robjs = tz.responses(resps, params.elec, params.daq); local random = tz.random(seeds); local drifter = tz.drifter(params.det.volumes, params.lar, random); local bagger = tz.bagger(params.daq); -local apasim(n) = - tz.apasim(anodes[n], pirs, params.det.volumes[n], - params.daq, params.adc, params.lar, - noisef, random); - -local simpipes = [apasim(n) for n in apaids]; +local oneapa(n) = + tz.sim(anodes[n], robjs.pirs, + params.daq, params.adc, params.lar, + noisef, 'adc', random); +local pipes = [oneapa(n) for n in apaids]; local frames = io.frame_save_npz("frames", output); local dump = io.frame_sink(); -local simbody = pg.fan.pipe('DepoSetFanout', simpipes, 'FrameFanin'); +local simbody = pg.fan.pipe('DepoSetFanout', pipes, 'FrameFanin'); local full = pg.pipeline([depos, drifter, bagger, simbody, frames, dump]); -tz.main(full) +tz.main(full, app) diff --git a/cfg/nf.jsonnet b/cfg/nf.jsonnet new file mode 100644 index 0000000..7a10551 --- /dev/null +++ b/cfg/nf.jsonnet @@ -0,0 +1,152 @@ +// Produce a noise filter component for an anode + +// This can be arbitrarily hairy and probably best to make a new file +// if substantial changes are needed. + +local wc = import "wirecell.jsonnet"; +local pg = import "pgraph.jsonnet"; + +function(anode, fieldresp, nsamples, tick=0.5*wc.us, rms_cuts=[]) { + local apaid = anode.data.ident, + + local chndb = { + type: 'OmniChannelNoiseDB', + name: 'ocndbperfect%d' % apaid, + uses: [anode, fieldresp], + data: { + anode: wc.tn(anode), + field_response: wc.tn(fieldresp), + tick: tick, + + // This sets the number of frequency-domain bins used in the noise + // filtering. It is not necessarily true that the time-domain + // waveforms have the same number of ticks. This must be non-zero. + nsamples: nsamples, + + // Group channels into their domains of coherency + groups: [ + std.range(apaid * 2560 + u * 40, apaid * 2560 + (u + 1) * 40 - 1) + for u in std.range(0, 19) + ] + [ + std.range(apaid * 2560 + 800 + v * 40, apaid * 2560 + 800 + (v + 1) * 40 - 1) + for v in std.range(0, 19) + ] + [ + std.range(apaid * 2560 + 1600 + w * 48, apaid * 2560 + 1600 + (w + 1) * 48 - 1) + for w in std.range(0, 19) + ], + + + // Overide defaults for specific channels. If an info is + // mentioned for a particular channel in multiple objects in this + // list then last mention wins. + channel_info: [ + // First entry provides default channel info across ALL + // channels. Subsequent entries override a subset of channels + // with a subset of these entries. There's no reason to + // repeat values found here in subsequent entries unless you + // wish to change them. + { + channels: std.range(apaid * 2560, (apaid + 1) * 2560 - 1), + nominal_baseline: 2048.0, // adc count + gain_correction: 1.0, // unitless + response_offset: 0.0, // ticks? + pad_window_front: 10, // ticks? + pad_window_back: 10, // ticks? + decon_limit: 0.02, + decon_limit1: 0.09, + adc_limit: 15, + roi_min_max_ratio: 0.8, // default 0.8 + min_rms_cut: 1.0, // units??? + max_rms_cut: 30.0, // units??? + + // parameter used to make "rcrc" spectrum + rcrc: 1.1 * wc.millisecond, // 1.1 for collection, 3.3 for induction + rc_layers: 1, // default 2 + + // parameters used to make "config" spectrum + reconfig: {}, + + // list to make "noise" spectrum mask + freqmasks: [], + + // field response waveform to make "response" spectrum. + response: {}, + }, + { + //channels: { wpid: wc.WirePlaneId(wc.Ulayer) }, + channels: std.range(apaid * 2560, apaid * 2560 + 800- 1), + response: { wpid: wc.WirePlaneId(wc.Ulayer) }, + response_offset: 120, // offset of the negative peak + pad_window_front: 20, + decon_limit: 0.02, + decon_limit1: 0.07, + roi_min_max_ratio: 3.0, + }, + { + //channels: { wpid: wc.WirePlaneId(wc.Vlayer) }, + channels: std.range(apaid * 2560 + 800, apaid * 2560 + 1600- 1), + response: { wpid: wc.WirePlaneId(wc.Vlayer) }, + response_offset: 124, + decon_limit: 0.01, + decon_limit1: 0.08, + roi_min_max_ratio: 1.5, + }, + { + //channels: { wpid: wc.WirePlaneId(wc.Wlayer) }, + channels: std.range(apaid * 2560 + 1600, apaid * 2560 + 2560- 1), + nominal_baseline: 400.0, + decon_limit: 0.05, + decon_limit1: 0.08, + }, + ] + rms_cuts, + }, // data + }, // chndb + + local single = { + type: 'pdOneChannelNoise', + name: 'ocn%d'%apaid, + data: { + noisedb: wc.tn(chndb), + anode: wc.tn(anode), + resmp: [ + {channels: std.range(2128, 2175), sample_from: 5996}, + {channels: std.range(1520, 1559), sample_from: 5996}, + {channels: std.range( 440, 479), sample_from: 5996}, + ], + }, + }, + + // In principle there may be multiple filters of each of each + // type. Define them above and collect them by type here. + local filters = { + channel: [ single, ], + group: [ ], + status: [ ], + }, + + local obnf = pg.pnode({ + + + type: 'OmnibusNoiseFilter', + name: 'nf%d'%apaid, + data: { + + // Nonzero forces the number of ticks in the waveform + nticks: 0, + + // channel bin ranges are ignored + // only when the channelmask is merged to `bad` + maskmap: {sticky: "bad", ledge: "bad", noisy: "bad"}, + channel_filters: [wc.tn(f) for f in filters.channel], + grouped_filters: [wc.tn(f) for f in filters.group], + channel_status_filters: [wc.tn(f) for f in filters.status], + noisedb: wc.tn(chndb), + intraces: 'orig%d' % apaid, // frame tag get all traces + outtraces: 'raw%d' % apaid, + }, + }, uses=[chndb, anode]+filters.channel+filters.group+filters.status, nin=1, nout=1), + + res: obnf + +}.res + diff --git a/cfg/sp.jsonnet b/cfg/sp.jsonnet new file mode 100644 index 0000000..a5928e4 --- /dev/null +++ b/cfg/sp.jsonnet @@ -0,0 +1,85 @@ +local wc = import "wirecell.jsonnet"; +local pg = import "pgraph.jsonnet"; + + +// Signal processing. +// +// Note, spfilt are a list of filter objects which MUST match +// hard-wired names in the C++, sorry. See, eg +// pgrapher/experiment/pdsp/sp-filters.jsonnet. +function(anode, fieldresp, elecresp, spfilt, adcpermv, perchan=null) { + local apaid = anode.data.ident, + + // if perchan file name is given we need to add this to a + // "uses" list and to set the name in OmnibusSigProc. + local pcresp = { + type: "PerChannelResponse", + data: { + filename: perchan + } + }, + local pcname = if std.type(perchan) == 'null' then "" else wc.tn(pcresp), + local pcuses = if std.type(perchan) == 'null' then [] else [pcresp], + + + local sigproc = pg.pnode({ + type: 'OmnibusSigProc', + name: 'sigproc%d' % apaid, + data: { + /** + * Optimized SP parameters (May 2019) + * Associated tuning in sp-filters.jsonnet + */ + anode: wc.tn(anode), + field_response: wc.tn(fieldresp), + elecresponse: wc.tn(elecresp), + ftoffset: 0.0, // default 0.0 + ctoffset: 1.0*wc.microsecond, // default -8.0 + per_chan_resp: pcname, + fft_flag: 0, // 1 is faster but higher memory, 0 is slightly slower but lower memory + postgain: 1.0, // default 1.2 + ADC_mV: adcpermv, // 4096 / (1400.0 * wc.mV), + troi_col_th_factor: 5.0, // default 5 + troi_ind_th_factor: 3.0, // default 3 + lroi_rebin: 6, // default 6 + lroi_th_factor: 3.5, // default 3.5 + lroi_th_factor1: 0.7, // default 0.7 + lroi_jump_one_bin: 1, // default 0 + + r_th_factor: 3.0, // default 3 + r_fake_signal_low_th: 375, // default 500 + r_fake_signal_high_th: 750, // default 1000 + r_fake_signal_low_th_ind_factor: 1.0, // default 1 + r_fake_signal_high_th_ind_factor: 1.0, // default 1 + r_th_peak: 3.0, // default 3.0 + r_sep_peak: 6.0, // default 6.0 + r_low_peak_sep_threshold_pre: 1200, // default 1200 + + // frame tags + wiener_tag: 'wiener%d' % apaid, + wiener_threshold_tag: 'threshold%d' % apaid, + decon_charge_tag: 'decon_charge%d' % apaid, + gauss_tag: 'gauss%d' % apaid, + + use_roi_debug_mode: false, + tight_lf_tag: 'tight_lf%d' % apaid, + loose_lf_tag: 'loose_lf%d' % apaid, + cleanup_roi_tag: 'cleanup_roi%d' % apaid, + break_roi_loop1_tag: 'break_roi_1st%d' % apaid, + break_roi_loop2_tag: 'break_roi_2nd%d' % apaid, + shrink_roi_tag: 'shrink_roi%d' % apaid, + extend_roi_tag: 'extend_roi%d' % apaid, + + use_multi_plane_protection: false, + mp3_roi_tag: 'mp3_roi%d' % apaid, + mp2_roi_tag: 'mp2_roi%d' % apaid, + + isWrapped: false, + sparse: false, + // process_planes: [0, 2], + } + }, nin=1, nout=1, uses=[anode, fieldresp, elecresp] + pcuses + spfilt), + + res: sigproc +}.res + diff --git a/cfg/toyzero.jsonnet b/cfg/toyzero.jsonnet index bab57f6..4445cd1 100644 --- a/cfg/toyzero.jsonnet +++ b/cfg/toyzero.jsonnet @@ -5,7 +5,6 @@ local pg = import "pgraph.jsonnet"; // define general object for toyzero { - protodune_params: import "pgrapher/experiment/pdsp/simparams.jsonnet", // return a "wireobj" wire_file(filename) : { @@ -25,55 +24,66 @@ local pg = import "pgraph.jsonnet"; } for vol in volumes], - // Return "PlaneImpactResponse" objects. daq and elec likely come - // from params. - pirs(respf, daq, elec): { - - local field_resp = { - type: "FieldResponse", - name: respf, - data: { - filename: respf - } - }, - - local binning = { nticks: daq.nticks, tick: daq.tick }, - - local rc_resp = { - type: "RCResponse", - data: binning { - width: 1.0*wc.ms, - } - }, - - local elec_resp = { - type: "ColdElecResponse", - data: binning { - shaping: elec.shaping, - gain: elec.gain, - postgain: elec.postgain, - }, - }, + field_response(filename) :: { + type: "FieldResponse", + data: { filename: filename } + }, + elec_response(shaping, gain, postgain, nticks, tick=0.5*wc.us) :: { + type: "ColdElecResponse", + data: { + shaping: shaping, + gain: gain, + postgain: postgain, + nticks: nticks, + tick: tick, + }, + }, + rc_response(width, nticks, tick=0.5*wc.us) :: { + type: "RCResponse", + data: { + width: width, + nticks: nticks, + tick: tick, + } + }, + + // Return "PlaneImpactResponse" objects. + // fr is field_response object. + // srs is list of short response objects, eg elec_resp + // lrs is list of long response objects, eg rc_response + pirs(fr, srs, lrs): { ret: [ { type: "PlaneImpactResponse", name : "PIRplane%d" % plane, data : { plane: plane, - field_response: wc.tn(field_resp), - short_responses: [wc.tn(elec_resp)], + field_response: wc.tn(fr), + short_responses: [wc.tn(r) for r in srs], // this needs to be big enough for convolving FR*CE overall_short_padding: 200*wc.us, - long_responses: [wc.tn(rc_resp)], + long_responses: [wc.tn(r) for r in lrs], // this needs to be big enough to convolve RC long_padding: 1.5*wc.ms, }, - uses: [field_resp, elec_resp, rc_resp], + uses: [fr] + srs + lrs, } for plane in [0,1,2]], - }.ret, + adcpermv(adc) :: + ((1 << adc.resolution)-1) / (adc.fullscale[1]-adc.fullscale[0]), + + responses(frfile, elec, daq, width=1.0*wc.ms) :: { + + fr: $.field_response(frfile), + er: $.elec_response(elec.shaping, elec.gain, elec.postgain, + daq.nticks, daq.tick), + rc: $.rc_response(width, daq.nticks, daq.tick), + pirs: $.pirs(self.fr, [self.er], [self.rc]) + }, + + default_seeds: [0, 1, 2, 3, 4], random(seeds = $.default_seeds) : { type: "Random", @@ -105,21 +115,53 @@ local pg = import "pgraph.jsonnet"; }, nin=1, nout=1), + // A per anode configure node for simulating noise. + noisesim(anode, noisef, daq, csdb=null, rnd=$.random()) : { + local apaid = anode.data.ident, + + local noise_model = { + type: "EmpiricalNoiseModel", + name: "emperical-noise-model-%d" % apaid, + data: { + anode: wc.tn(anode), + chanstat: if std.type(csdb) == "null" then "" else wc.tn(csdb), + spectra_file: noisef, + nsamples: daq.nticks, + period: daq.tick, + wire_length_scale: 1.0*wc.cm, // optimization binning + }, + uses: [anode] + if std.type(csdb) == "null" then [] else [csdb], + }, + ret: pg.pnode({ + type: "AddNoise", + name: "addnoise-" + noise_model.name, + data: { + rng: wc.tn(rnd), + model: wc.tn(noise_model), + nsamples: daq.nticks, + replacement_percentage: 0.02, // random optimization + }}, nin=1, nout=1, uses=[rnd, noise_model]), + }.ret, - // A pipeline of nodes to simulate one APA. - // - // The vol, daq, adc, lar likely comes from params. - // The noisef should be a file name. - // fixme: probably should be broken up... - apasim(anode, pirs, vol, daq, adc, lar, noisef=null, tier='adc', rnd=$.random()) : { + digisim(anode, adc) :: { + local apaid = anode.data.ident, + ret: pg.pnode({ + type: "Digitizer", + name: 'Digitizer%d' % apaid, + data : adc { + anode: wc.tn(anode), + frame_tag: "orig%d"%apaid, + } + }, nin=1, nout=1, uses=[anode]), + }.ret, - local tagbase = if tier == 'adc' then 'orig' else 'volt', + sigsim(anode, pirs, daq, lar, rnd=$.random()) : { local apaid = anode.data.ident, local ductor = pg.pnode({ type:'DepoTransform', - name:'DepoTransformt%d' % apaid, + name:'DepoTransform%d' % apaid, data: { rng: wc.tn(rnd), anode: wc.tn(anode), @@ -147,50 +189,36 @@ local pg = import "pgraph.jsonnet"; }, }, nin=1, nout=1), - local digitizer = pg.pnode({ - type: "Digitizer", - name: 'Digitizer%d' % apaid, - data : adc { - anode: wc.tn(anode), - frame_tag: "%s%d"%[tagbase, apaid], - } - }, nin=1, nout=1, uses=[anode]), + ret: pg.pipeline([ductor, reframer]), + }.ret, - + // A kitchen sink pipeline of nodes to simulate one APA. + // + // The daq, adc, lar likely comes from params. + // + // Fullest chain is sig + noise -> adc + // + // If no lar or pirs is given, then no signal. + // If no noisef given, then no noise. + // If no adc given, then no digitizer + // The tier can be 'adc' or something else if no digitizer. + sim(anode, pirs, daq, adc, lar, noisef=null, tier='adc', rnd=$.random()) : { + + // fixme: make configurable local csdb = null, - local noise_model = { - type: "EmpiricalNoiseModel", - name: "emperical-noise-model-%d" % apaid, - data: { - anode: wc.tn(anode), - chanstat: if std.type(csdb) == "null" then "" else wc.tn(csdb), - spectra_file: noisef, - nsamples: daq.nticks, - period: daq.tick, - wire_length_scale: 1.0*wc.cm, // optimization binning - }, - uses: [anode] + if std.type(csdb) == "null" then [] else [csdb], - }, - local noise = pg.pnode({ - type: "AddNoise", - name: "addnoise-" + noise_model.name, - data: { - rng: wc.tn(rnd), - model: wc.tn(noise_model), - nsamples: daq.nticks, - replacement_percentage: 0.02, // random optimization - }}, nin=1, nout=1, uses=[rnd, noise_model]), - - local beg = [ductor, reframer], + local beg = if std.type(lar) == "null" || std.type(pirs) == "null" then [] else [ + $.sigsim(anode, pirs, daq, lar, rnd)], - local mid = if std.type(noisef) == "null" then [] else [noise], + local mid = if std.type(noisef) == "null" then [] else [ + $.noisesim(anode, noisef, daq, rnd, csdb)], - local end = if tier == 'adc' then [digitizer] else [], + local end = if tier == 'adc' then [$.digisim(anode, adc)] else [], pipeline: pg.pipeline(beg + mid + end), }.pipeline, + local plugins = [ "WireCellSio", "WireCellAux", "WireCellGen", "WireCellSigProc", From aa660bb2eaa67b3ba798cc62e3bc8163caa33401 Mon Sep 17 00:00:00 2001 From: Brett Viren Date: Wed, 21 Jul 2021 16:49:50 -0400 Subject: [PATCH 03/15] Sigproc working and with per-apa output files --- README.org | 30 +- Snakefile | 73 +- cfg/main-depos-sigproc.jsonnet | 29 +- index.html | 75 +- toyzero-all-dag.dot | 410 +++--- toyzero-all-dag.pdf | Bin 26783 -> 27329 bytes toyzero-all-dag.svg | 2436 ++++++++++++++++---------------- 7 files changed, 1565 insertions(+), 1488 deletions(-) diff --git a/README.org b/README.org index 00b1488..228ea67 100644 --- a/README.org +++ b/README.org @@ -291,6 +291,28 @@ The ~all_frames~ target generates "frame" data from depos by running the Wire-Cell simulation. The "frame" file format is described elsewhere. For here, we treat it as a temporary. +The simulation is internally structured as a DAG of components +exchanging data flow as shown: + +#+ATTR_HTML: :width 90% +[[file:plots/dots/depos-sim-adc/dag.png]] + +Frames come in different flavor depending on the final output data +tier. We name and describe them as: + +- noiseless :: these are integer ADC waveforms reflecting existence of + only ionization electrons and no electronics noise. They are + bipolar on the induction planes "U" and "V and unipolar on + collection plane "W". They have a fixed "baseline" at an ADC value + depending on the plane and are sparse (baseline-padded) at locations + away from any ionization. + +- signal :: these floating point measures of the original ionization + electrons after signal processing and noise filtering is applied to + signal and noise simulation. The waveforms from all planes are + unipolar and give a measure of the original ionization distribution. + The waveforms have a "baseline" of 0.0 and are sparse + (baseline-padded) at locations away from any ionization. ** images :PROPERTIES: @@ -308,8 +330,8 @@ match. For example: protodune-orig-0-1-W (960, 6000) #+end_example -These image arrays have shape ~(nchan, ntick)~. That is each row is the -waveform from one channel and has ~ntick=6000~ samples (3ms). When +These image arrays have shape ~(nchan, ntick)~. That is, each row is +the waveform from one channel and has ~ntick=6000~ samples (3ms). When visualized with matplotlib's ~imshow()~ you will see channels as Y-axis, tics as X-axis. @@ -319,6 +341,10 @@ This "W" file holds one array of 960 channels and 6000 sample time induction planes and each will have 800 channels and the contemporaneous 6000 ticks. +Like frames above, images come in corresponding flavors. See section +[[frames]] for description. + + * Plotting :PROPERTIES: :CUSTOM_ID: plotting diff --git a/Snakefile b/Snakefile index 3f87317..371699b 100644 --- a/Snakefile +++ b/Snakefile @@ -22,9 +22,13 @@ seed = config.get("seed", "1,2,3,4") ntracks = config.get("ntracks", 10) nevents = config.get("nevents", 10) wcloglvl = config.get("wcloglvl", "info") + +tiers = config.get("tiers", ["noiseless"]) + # print(f"OUTDIR:{outdir}") # print(f"NEVENTS:{nevents}") # print(f"WCLOGLVL:{wcloglvl}") +print(f"TIERS:{tiers}, {type(tiers)}") # The rest are hard wired for now wcdata_url = "https://github.com/WireCell/wire-cell-data/raw/master" @@ -39,13 +43,20 @@ wcdata_ext = "json.bz2" resps = "dune-garfield-1d565" wires = "protodune-wires-larsoft-v4" +# The data domains describe a universe. For toyzero, they are +# associated with a particular detector response. +DOMAINS = ["fake", "real"] + +# The data tiers for frame or image +TIERS = ["noiseless", "signal"] + # some important file names real_resps = f'{datadir}/resps/real-resps.{wcdata_ext}' fake_resps = f'{datadir}/resps/fake-resps.{wcdata_ext}' domain_resps = f'{datadir}/resps/{{domain}}-resps.{wcdata_ext}' wires_file = f'{datadir}/wires/wires.{wcdata_ext}' depos_file = f'{datadir}/depos/depos.npz' -domain_frames = f'{datadir}/frames/{{domain}}-frames.npz' +domain_frames = f'{datadir}/frames/{{tier}}/{{domain}}-frames.npz' # resp - prepare response files @@ -167,15 +178,24 @@ rule all_depos: # frames -rule sim_dots: +def wct_cfg_file(w): + slugs = dict(signal="depos-sigproc", + noiseless="depos-sim-adc") + slug = slugs[w.tier] + return f'cfg/main-{slug}.jsonnet' + + +# note, passes bogus TLAs so don't use the genearted json! +rule wct_dots: input: - config = 'cfg/main-depos-sim-adc.jsonnet' + config = wct_cfg_file output: - json = f'{plotdir}/sim-graph.json', - dot = f'{plotdir}/sim-graph.dot', - png = f'{plotdir}/sim-graph.png', - pdf = f'{plotdir}/sim-graph.pdf' + json = temp(f'{plotdir}/dots/{{tier}}/cfg.json'), + dot = temp(f'{plotdir}/dots/{{tier}}/dag.dot'), + png = f'{plotdir}/dots/{{tier}}/dag.png', + pdf = f'{plotdir}/dots/{{tier}}/dag.pdf' shell: ''' + mkdir -p {plotdir}/dots/{wildcards.tier}; wcsonnet \ -P cfg \ -A input=DEPOS-FILE \ @@ -183,17 +203,20 @@ rule sim_dots: -A wires=WIRES-FILE \ -A resps=RESPS-FILE \ {input.config} > {output.json}; - wirecell-pgraph dotify --jpath=-1 {output.json} {output.dot} ; + wirecell-pgraph dotify --no-params --jpath=-1 {output.json} {output.dot} ; dot -Tpng -o {output.png} {output.dot} ; dot -Tpdf -o {output.pdf} {output.dot} ''' +rule all_dots: + input: + expand(rules.wct_dots.output, tier=tiers) rule sim_frames: input: wires = wires_file, resps = domain_resps, depos = depos_file, - config = 'cfg/main-depos-sim-adc.jsonnet' + config = wct_cfg_file output: frames = temp(domain_frames) shell: ''' @@ -216,7 +239,7 @@ rule plot_frames: input: domain_frames output: - f'{plotdir}/frames-{{domain}}-apa{{apa}}.{{ext}}' + f'{plotdir}/frames-{{tier}}-{{domain}}-apa{{apa}}.{{ext}}' params: p = gen_plot_frames shell:''' @@ -224,9 +247,9 @@ rule plot_frames: ''' rule plot_frames_hidpi: input: - f'{plotdir}/frames-{{domain}}-apa{{apa}}.pdf' + f'{plotdir}/frames-{{tier}}-{{domain}}-apa{{apa}}.pdf' output: - f'{plotdir}/hidpi/frames-{{domain}}-apa{{apa}}.png' + f'{plotdir}/hidpi/frames-{{tier}}-{{domain}}-apa{{apa}}.png' params: shell:''' @@ -236,11 +259,13 @@ rule plot_frames_hidpi: rule all_frames: input: - expand(rules.sim_frames.output, domain=["real","fake"]), + expand(rules.sim_frames.output, domain=["real","fake"], + tier=tiers), expand(rules.plot_frames.output, domain=["real","fake"], + tier=tiers, ext=["png","pdf"], apa=list(range(6))), expand(rules.plot_frames_hidpi.output, domain=["real","fake"], - apa=[0]) + tier=tiers, apa=[0]) @@ -255,7 +280,7 @@ rule all_frames: ## static data (ie, defined right here). So, that is what we do. # split_outer_product = dict( - domain = ["protodune"], +# domain = ["protodune"], event = list(range(nevents)), apa = list(range(6)), plane = ["U","V","W"], @@ -265,11 +290,11 @@ rule split_images: input: domain_frames output: - expand(datadir+'/images/{{domain}}/protodune-orig-{event}-{apa}-{plane}.npz', + expand(datadir+'/images/{{tier}}/{{domain}}/protodune-orig-{event}-{apa}-{plane}.npz', **split_outer_product) shell: ''' wirecell-util frame-split \ - -f {datadir}/images/{wildcards.domain}/{{detector}}-{{tag}}-{{index}}-{{anodeid}}-{{planeletter}}.npz \ + -f {datadir}/images/{wildcards.tier}/{wildcards.domain}/{{detector}}-{{tag}}-{{index}}-{{anodeid}}-{{planeletter}}.npz \ {input} ''' @@ -278,16 +303,16 @@ def gen_title(w): dim='2D' else: dim='q1D' - return f'"{w.domain}/{dim}, event {w.event}, APA {w.apa}, {w.plane} plane"', + return f'"{w.tier} {w.domain}/{dim}, event {w.event}, APA {w.apa}, {w.plane} plane"', ## Note, we must match the input here by hand to the output above ## because the domain is not included in the expand above but is here. ## Above is 1->N, here is 1->1. rule plot_split_images: input: - datadir+'/images/{domain}/protodune-orig-{event}-{apa}-{plane}.npz', + datadir+'/images/{tier}/{domain}/protodune-orig-{event}-{apa}-{plane}.npz', output: - plotdir+'/images/{domain}/{cmap}/protodune-orig-{event}-{apa}-{plane}.{ext}' + plotdir+'/images/{tier}/{domain}/{cmap}/protodune-orig-{event}-{apa}-{plane}.{ext}' params: title = gen_title shell: ''' @@ -302,10 +327,12 @@ rule plot_split_images: ## note, list-of-list for the split_images rule rule all_images: input: - expand(rules.split_images.output, domain=["real","fake"]), + expand(rules.split_images.output, + domain=["real","fake"], tier=tiers), expand( rules.plot_split_images.output, domain = ["real","fake"], + tier = tiers, event = [0], apa=[2], plane=["U"], ext = ["png", "pdf", "svg"], cmap = ["seismic", "Spectral", "terrain", "coolwarm", "viridis"], @@ -313,7 +340,9 @@ rule all_images: rule just_images: input: - expand(rules.split_images.output, domain=["real","fake"]), + expand(rules.split_images.output, + domain=["real","fake"], + tier=tiers) rule all: input: diff --git a/cfg/main-depos-sigproc.jsonnet b/cfg/main-depos-sigproc.jsonnet index 9edb6e2..847afca 100644 --- a/cfg/main-depos-sigproc.jsonnet +++ b/cfg/main-depos-sigproc.jsonnet @@ -53,19 +53,32 @@ local sim(n) = local adcpermv = tz.adcpermv(params.adc); local nfsp(n) = pg.pipeline([ - nf(anodes[n], robjs.fr, params.daq.nticks, params.daq.tick), + //nf(anodes[n], robjs.fr, params.daq.nticks, params.daq.tick), sp(anodes[n], robjs.fr, robjs.er, spfilt, adcpermv)]); -local oneapa(n) = pg.pipeline([sim(n), nfsp(n)]); +local outfile(n) = { + local l = std.split(output,"."), + ret:"%s-apa%d.%s"%[l[0],n,l[1]] +}.ret; +local oneapa(n) = { + local name = "gauss%d"%n, + local outf = outfile(n), + pipe: pg.pipeline([ + sim(n), nfsp(n), + io.frame_save_npz(name, outf, digitize=false, tags=[name]), + io.frame_sink(name)]) +}.pipe; local pipes = [oneapa(n) for n in apaids]; -local frame_tags = ["gaus%d"%n for n in apaids]; -local frames = io.frame_save_npz("frames", output, - digitize = false, tags=frame_tags); -local dump = io.frame_sink(); +// local frame_tags = ["gauss%d"%n for n in apaids]; +// local frames = io.frame_save_npz("frames", output, +// digitize = false, tags=frame_tags); +// local dump = io.frame_sink(); +// local body = pg.fan.pipe('DepoSetFanout', pipes, 'FrameFanin', +// outtags=frame_tags); -local body = pg.fan.pipe('DepoSetFanout', pipes, 'FrameFanin'); -local full = pg.pipeline([depos, drifter, bagger, body, frames, dump]); +local body = pg.fan.fanout('DepoSetFanout', pipes); +local full = pg.pipeline([depos, drifter, bagger, body]); tz.main(full, app) diff --git a/index.html b/index.html index e39dfc5..d2b8e5c 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + LS4GAN's Toy Zero @@ -257,7 +257,7 @@

Table of Contents

-The toyzero package provides first steps toward LS4GAN. +The toyzero package provides first steps toward LS4GAN. See also next-steps.html

@@ -334,7 +334,7 @@

2.1 Environment

A one time setup of direnv:

-
+
 $ cd toyzero
 $ cp dot.envrc .envrc
 $ emacs .envrc  # edit to taste
@@ -352,7 +352,7 @@ 
2.2 Check Wire-Cell Toolki
 Check if WCT is available with these commands:
 

 
-
+
 $ wire-cell --help
 $ wcsonnet wirecell.jsonnet
 $ echo $WIRECELL_PATH
@@ -374,7 +374,7 @@ 
2.3 Python

 various other Python 3 packages are required.  
 

 
-
+
 $ cd toyzero
 $ pip install -r requirements.txt
 

@@ -383,7 +383,7 @@ 
2.3 Python

 Some checks:
 

 
-
+
 $ wirecell-<TAB>
 $ wirecell-util --help
 $ snakemake --help
@@ -406,7 +406,7 @@ 
3 Usage

 need run only:
 

 
-
+
 $ snakemake -jall all
 

 
@@ -415,7 +415,7 @@ 
3 Usage

 To see what is produced:
 

 
-
+
 $ tree data plots
 

 
@@ -424,7 +424,7 @@ 
3 Usage

 you can do:
 

 
-
+
 $ snakemake -jall just_images
 

 
@@ -435,7 +435,7 @@ 
3 Usage

 may run as:
 

 
-
+
 $ snakemake -jall just_images --notemp
 

 
@@ -460,7 +460,7 @@ 
4 Details

 manner:
 

 
-
+
 $ snakemake -jall all_resp
 $ snakemake -jall all_wires
 $ snakemake -jall all_depos
@@ -506,7 +506,7 @@ 
4.1 resp

 
 
 
-

+

 
fake-resps-diagnostic.png
 

 

@@ -516,7 +516,7 @@ 
4.1 resp

 
 
 
-

+

 
real-resps-diagnostic.png
 

 

@@ -549,7 +549,7 @@ 
4.3 depos

 for input to the WCT simulation.  It produces a file:
 

 
-
+
 data/depos/depos.npz
 

 
@@ -557,7 +557,7 @@ 
4.3 depos

 The file is in Numpy format with three types of arrays named like:
 

 
-
+
 depo_data_<N>
 depo_info_<N>
 track_info_<N>
@@ -590,7 +590,7 @@ 
4.3 depos

 

 
 
-

+

 
depos-diagnostic.png
 

 

@@ -624,9 +624,18 @@ 
4.4 frames

 Wire-Cell simulation.  The "frame" file format is described elsewhere.
 For here, we treat it as a temporary.
 

+
+

+The simulation is internally structured as a DAG as shown:
+

+
+
+

+
dag.png
+

+

 

 

-
 
 

 
4.5 images

@@ -638,7 +647,7 @@ 
4.5 images

 match.  For example:
 

 
-
+
 ❯ wirecell-util npzls data/images/real/protodune-orig-0-1-W.npz 
 protodune-orig-0-1-W (960, 6000)
 

@@ -698,7 +707,7 @@ 
5.1 Image formats

 

 
 
-

+

 
frames-fake-apa0.png
 

 

@@ -708,7 +717,7 @@ 
5.1 Image formats

 

 
 
-

+

 
frames-fake-apa0.png
 

 

@@ -717,7 +726,7 @@ 
5.1 Image formats

 

 If you need more zoom from your evince PDF viewer try
 

-
+
 ❯ gsettings set org.gnome.Evince page-cache-size 2014
 

 

@@ -747,7 +756,7 @@ 
5.2 Color maps

 as command line options:
 

 
-
+
 ❯ wirecell-util npz-to-img --help
 Usage: wirecell-util npz-to-img [OPTIONS] NPZFILE
 
@@ -782,7 +791,7 @@ 
5.2 Color maps

 
 
 
-

+

 
protodune-orig-0-2-U.png
 

 

@@ -792,7 +801,7 @@ 
5.2 Color maps

 
 
 
-

+

 
protodune-orig-0-2-U.png
 

 

@@ -802,7 +811,7 @@ 
5.2 Color maps

 
 
 
-

+

 
protodune-orig-0-2-U.png
 

 

@@ -812,7 +821,7 @@ 
5.2 Color maps

 
 
 
-

+

 
protodune-orig-0-2-U.png
 

 

@@ -833,7 +842,7 @@ 
5.3 Real vs Fake

 
 
 
-

+

 

 Sorry, your browser does not support SVG.
 

@@ -845,7 +854,7 @@ 
5.3 Real vs Fake

 
 
 
-

+

 

 Sorry, your browser does not support SVG.
 

@@ -891,7 +900,7 @@ 
6 Configuration

 To customize,
 

 
-
+
 $ cp toyzero.yaml mycfg.yaml
 $ emacs mycfg.yaml
 $ snakemake -jall --configfile mycfg.yaml all
@@ -907,7 +916,7 @@ 
6 Configuration

 You may also customize specific parameters from the command line:
 

 
-
+
 $ snakemake -jall --config outdir=junk ntracks=10 all_depos
 $ eom junk/plots/depos-diagnostic.png 
 

@@ -948,7 +957,7 @@ 
7 Snakemake

 

 
 
-

+

 

 Sorry, your browser does not support SVG.
 

@@ -974,7 +983,7 @@ 
8 Hacking

 so like:
 

 
-
+
 $ git clone git@github.com:wirecell/wire-cell-python.git
 $ cd wire-cell-python/
 $ pip install -U -e .
@@ -990,7 +999,7 @@ 
8 Hacking

 

 

 
Author: BV

-
Created: 2021-07-20 Tue 10:49

+
Created: 2021-07-21 Wed 15:18

 
Validate

 

 
diff --git a/toyzero-all-dag.dot b/toyzero-all-dag.dot
index ba373d9..3c12237 100644
--- a/toyzero-all-dag.dot
+++ b/toyzero-all-dag.dot
@@ -2,214 +2,214 @@ digraph snakemake_dag {
     graph[bgcolor=white, margin=0];
     node[shape=box, style=rounded, fontname=sans,                 fontsize=10, penwidth=2];
     edge[penwidth=2, color=grey];
-	0[label = "just_images", color = "0.17 0.6 0.85", style="rounded"];
-	1[label = "split_images", color = "0.37 0.6 0.85", style="rounded"];
-	2[label = "sim_frames\ndomain: real", color = "0.60 0.6 0.85", style="rounded"];
-	3[label = "get_wires", color = "0.43 0.6 0.85", style="rounded"];
-	4[label = "get_resp_real", color = "0.13 0.6 0.85", style="rounded"];
-	5[label = "gen_depos", color = "0.23 0.6 0.85", style="rounded"];
-	6[label = "split_images", color = "0.37 0.6 0.85", style="rounded"];
-	7[label = "sim_frames\ndomain: fake", color = "0.60 0.6 0.85", style="rounded"];
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 }            
diff --git a/toyzero-all-dag.pdf b/toyzero-all-dag.pdf
index 3673f63dc8842518805b519adfb0ce4b317900a3..17ad3849b49efa47a560f09f2b275efb32f14148 100644
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+apa: 2
+cmap: seismic
+event: 0
+ext: png
+plane: U
+
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+40
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+plot_split_images
+apa: 2
+cmap: Spectral
+event: 0
+ext: png
+plane: U
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+apa: 2
+cmap: terrain
+event: 0
+ext: png
+plane: U
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+plot_split_images
+apa: 2
+cmap: coolwarm
+event: 0
+ext: png
+plane: U
+
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+
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+apa: 2
+cmap: viridis
+event: 0
+ext: png
+plane: U
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+apa: 2
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+event: 0
+ext: pdf
+plane: U
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+apa: 2
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+event: 0
+ext: pdf
+plane: U
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+apa: 2
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+event: 0
+ext: pdf
+plane: U
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+apa: 2
+cmap: coolwarm
+event: 0
+ext: pdf
+plane: U
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+apa: 2
+cmap: viridis
+event: 0
+ext: pdf
+plane: U
+
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+apa: 2
+cmap: seismic
+event: 0
+ext: svg
+plane: U
+
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+apa: 2
+cmap: Spectral
+event: 0
+ext: svg
+plane: U
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+apa: 2
+cmap: terrain
+event: 0
+ext: svg
+plane: U
+
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+apa: 2
+cmap: coolwarm
+event: 0
+ext: svg
+plane: U
+
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+apa: 2
+cmap: viridis
+event: 0
+ext: svg
+plane: U
+
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+apa: 2
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+event: 0
+ext: png
+plane: U
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+plot_split_images
+apa: 2
+cmap: Spectral
+event: 0
+ext: png
+plane: U
+
+
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+
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+plot_split_images
+apa: 2
+cmap: terrain
+event: 0
+ext: png
+plane: U
+
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+
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+plot_split_images
+apa: 2
+cmap: coolwarm
+event: 0
+ext: png
+plane: U
+
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+38->57
+
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+
+plot_split_images
+apa: 2
+cmap: viridis
+event: 0
+ext: png
+plane: U
+
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+
+38->58
+
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+
+plot_split_images
+apa: 2
+cmap: seismic
+event: 0
+ext: pdf
+plane: U
+
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+38->59
+
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+plot_split_images
+apa: 2
+cmap: Spectral
+event: 0
+ext: pdf
+plane: U
+
+
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+38->60
+
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+
+plot_split_images
+apa: 2
+cmap: terrain
+event: 0
+ext: pdf
+plane: U
+
+
+
+38->61
+
+
+
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+
+plot_split_images
+apa: 2
+cmap: coolwarm
+event: 0
+ext: pdf
+plane: U
+
+
+
+38->62
+
+
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+
+plot_split_images
+apa: 2
+cmap: viridis
+event: 0
+ext: pdf
+plane: U
+
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+38->63
+
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+plot_split_images
+apa: 2
+cmap: seismic
+event: 0
+ext: svg
+plane: U
+
+
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+38->64
+
+
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+65
+
+plot_split_images
+apa: 2
+cmap: Spectral
+event: 0
+ext: svg
+plane: U
+
+
+
+38->65
+
+
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+66
+
+plot_split_images
+apa: 2
+cmap: terrain
+event: 0
+ext: svg
+plane: U
+
+
+
+38->66
+
+
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+67
+
+plot_split_images
+apa: 2
+cmap: coolwarm
+event: 0
+ext: svg
+plane: U
+
+
+
+38->67
+
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+
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+apa: 2
+cmap: viridis
+event: 0
+ext: svg
+plane: U
+
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From c5faa98f98718e4c2abe28c32f78fa4081a83a80 Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Fri, 23 Jul 2021 13:09:47 -0400
Subject: [PATCH 04/15] Checkpoint

---
 Snakefile                      |  43 ++++++++---
 cfg/ioutils.jsonnet            |  41 +++++++++-
 cfg/main-depos-sigproc.jsonnet | 137 +++++++++++++++++++--------------
 cfg/main-depos-sim.jsonnet     |  63 +++++++++++++++
 cfg/nf.jsonnet                 |  99 +-----------------------
 cfg/pdsp_chndb.jsonnet         | 106 +++++++++++++++++++++++++
 cfg/sp.jsonnet                 |   1 -
 cfg/toyzero.jsonnet            |  12 ++-
 cfg/utils.jsonnet              |  12 +++
 dot.envrc                      |   1 +
 testit.sh                      |  43 +++++++++++
 11 files changed, 380 insertions(+), 178 deletions(-)
 create mode 100644 cfg/main-depos-sim.jsonnet
 create mode 100644 cfg/pdsp_chndb.jsonnet
 create mode 100644 cfg/utils.jsonnet
 create mode 100755 testit.sh

diff --git a/Snakefile b/Snakefile
index 371699b..0fb5631 100644
--- a/Snakefile
+++ b/Snakefile
@@ -42,6 +42,8 @@ wcdata_ext = "json.bz2"
 ## to span some set of each.
 resps = "dune-garfield-1d565"
 wires = "protodune-wires-larsoft-v4"
+# a few places want a list of APA IDs
+apa_iota = list(range(6))
 
 # The data domains describe a universe.  For toyzero, they are
 # associated with a particular detector response.
@@ -56,7 +58,6 @@ fake_resps    = f'{datadir}/resps/fake-resps.{wcdata_ext}'
 domain_resps  = f'{datadir}/resps/{{domain}}-resps.{wcdata_ext}'
 wires_file    = f'{datadir}/wires/wires.{wcdata_ext}'
 depos_file    = f'{datadir}/depos/depos.npz'
-domain_frames = f'{datadir}/frames/{{tier}}/{{domain}}-frames.npz'
 
 # resp - prepare response files
 
@@ -199,7 +200,7 @@ rule wct_dots:
     wcsonnet \
     -P cfg \
     -A input=DEPOS-FILE \
-    -A output=FRAMES-FILE \
+    --tla-code taps='{{"orig":"frame-orig-.npz","gauss":"frame-gauss.npz"}}' \
     -A wires=WIRES-FILE \
     -A resps=RESPS-FILE \
     {input.config} > {output.json};
@@ -211,6 +212,19 @@ rule all_dots:
     input:
         expand(rules.wct_dots.output, tier=tiers)
 
+# this gives the pattern for one per-APA frame file.  The %d is
+# interpolated by wire-cell configuration.
+frames_pattern = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa%d.npz'
+frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.npz'
+
+def frame_taps(w):
+    if w.tier == "noiseless":
+        tap = "orig"
+    else:
+        tap = "gauss"
+    fp = frames_pattern.format(**dict(w))
+    return dict(tap=tap, pat=fp)
+
 rule sim_frames:
     input:
         wires = wires_file,
@@ -218,14 +232,16 @@ rule sim_frames:
         depos = depos_file,
         config = wct_cfg_file
     output:
-        frames = temp(domain_frames)
+        temp([frames_pattern%n for n in apa_iota])
+    params:
+        p = frame_taps
     shell: '''
-    rm -f {output.frames}; 
+    rm -f {output}; 
     wire-cell \
     -l stdout -L {config[wcloglvl]} \
     -P cfg \
     -A input={input.depos} \
-    -A output={output.frames} \
+    --tla-code 'taps={{"{params.p[tap]}":"{params.p[pat]}"}}' \
     -A wires={input.wires} \
     -A resps={input.resps} \
     -c {input.config}
@@ -233,18 +249,23 @@ rule sim_frames:
         
 def gen_plot_frames(w):
     i = int(w.apa)
-    return dict(chb=f'{i},{i+2560}')
+    if w.tier == "noiseless":
+        return dict(chb=f'{i},{i+2560}', tag="")
+    if w.tier == "signal":
+        tag = f"gauss{i}"
+        return dict(chb=f'0,2560', tag=tag)
 
 rule plot_frames:
     input:
-        domain_frames
+        frames_wildcard
     output:
         f'{plotdir}/frames-{{tier}}-{{domain}}-apa{{apa}}.{{ext}}'
     params:
         p = gen_plot_frames
     shell:'''
-    wirecell-gen plot-sim {input} {output} -p frames -b {params.p[chb]}
+    wirecell-gen plot-sim {input} {output} -p frames -b {params.p[chb]} --tag "{params.p[tag]}"
     '''
+
 rule plot_frames_hidpi:
     input:
         f'{plotdir}/frames-{{tier}}-{{domain}}-apa{{apa}}.pdf'
@@ -263,7 +284,7 @@ rule all_frames:
                tier=tiers),
         expand(rules.plot_frames.output, domain=["real","fake"],
                tier=tiers,
-               ext=["png","pdf"], apa=list(range(6))),
+               ext=["png","pdf"], apa=apa_iota),
         expand(rules.plot_frames_hidpi.output, domain=["real","fake"],
                tier=tiers, apa=[0])
 
@@ -282,13 +303,13 @@ rule all_frames:
 split_outer_product = dict(
 #    domain = ["protodune"],
     event  = list(range(nevents)),
-    apa    = list(range(6)),
+    apa    = apa_iota,
     plane  = ["U","V","W"],
 )
 
 rule split_images:
     input:
-        domain_frames
+        frames_wildcard
     output:
         expand(datadir+'/images/{{tier}}/{{domain}}/protodune-orig-{event}-{apa}-{plane}.npz',
                **split_outer_product)
diff --git a/cfg/ioutils.jsonnet b/cfg/ioutils.jsonnet
index 0688771..16f0a2b 100644
--- a/cfg/ioutils.jsonnet
+++ b/cfg/ioutils.jsonnet
@@ -1,8 +1,11 @@
 local wc = import "wirecell.jsonnet";
-local g = import 'pgraph.jsonnet';
+local pg = import 'pgraph.jsonnet';
+
+local ut = import 'utils.jsonnet';
+
 {
     // Return a numpy depo source configuration.
-    npz_source_depo(name, filename) :: g.pnode({
+    npz_source_depo(name, filename) :: pg.pnode({
         type: 'NumpyDepoLoader',
         name: name,
         data: {
@@ -12,7 +15,7 @@ local g = import 'pgraph.jsonnet';
 
 
     // Return a numpy frame saver configuration.
-    frame_save_npz(name, filename, digitize=true, tags=[]) :: g.pnode({
+    frame_save_npz(name, filename, digitize=true, tags=[]) :: pg.pnode({
         type: 'NumpyFrameSaver',
         name: name,
         data: {
@@ -22,8 +25,38 @@ local g = import 'pgraph.jsonnet';
         }}, nin=1, nout=1),
 
     // Use to cap off a frame stream with a sink.
-    frame_sink(name="frame-sink") :: g.pnode({
+    frame_sink(name="frame-sink") :: pg.pnode({
         type: "DumpFrames",
         name: name,
     }, nin=1, nout=0),    
+
+
+    // Save frames to outfile.
+    //
+    // name, outfile and elements of the tags list may have a single
+    // "%" format code which if it exists will be interpolated again
+    // the "index".
+    //
+    // If outfile has not "%" format the string "-apa%d" will be
+    // appended to the base file name (prior to .ext).
+    //
+    // The "name" is used to give unique objects.
+    //
+    // The tags determine which among all available frames/trace tags
+    // to save.
+    //
+    // If digitize is true, frame samples will be truncated to int
+    // else left as float.
+    //
+    // If cap is false, the resulting node acts as a filter.
+    frame_out(name, index, outfile, tags=["gauss%d"], digitize=false, cap=true) :: {
+        local nam = if ut.haspct(name) then name%index else name,
+        local tint = [if ut.haspct(t) then t%index else t for t in tags],
+        local end = if cap then [$.frame_sink(nam)] else [],
+        local outf = if ut.haspct(outfile) then outfile%index else ut.basename_append(outfile, "-apa%d"%index),
+
+        ret: pg.pipeline([$.frame_save_npz(nam, outf, digitize=digitize, tags=tint)]
+                         + end)
+    }.ret,
+    
 }
diff --git a/cfg/main-depos-sigproc.jsonnet b/cfg/main-depos-sigproc.jsonnet
index 847afca..f04e45d 100644
--- a/cfg/main-depos-sigproc.jsonnet
+++ b/cfg/main-depos-sigproc.jsonnet
@@ -3,20 +3,35 @@
 // It implements the chain:
 //   (depos)->sim(signal,noise)->sigproc->(signals)
 //
-// It takes a number of top-level-arguments (TLA).
+// It takes a number of top-level-arguments (TLA) which can control
+// input configuration and input data and a number of output data
+// "taps".  You may also control if it runs in single or multi thread
+// mode
 //
 // Run like
 //
 //  wire-cell \
-//    -A input=depos.npz -A output=frames.npz \
+//    -A depos=depos.npz \
+//    -A taps={...see below...} \
 //    -A wires=wires-geometry.json.bz2 \
 //    -A resps=field-response.json.bz2 \
 //    -A noisef=/path/to/noise/model/file \
-//    -A app=[Pgrapher|TbbFlow] \
+//    -A thread=[single|multi] \
 //    -c main-depos-sim-adc.jsonnet
 //
-// The 'noisef' TLA is optional and specifies a noise model.  If not
-// given, only signal is simulated.
+// The 'noisef' TLA is optional and specifies a noise model file.  If
+// not given, only signal is simulated.
+//
+// If "taps" is given it specifies a mapping from a data tier key word
+// to a file name.  The key is one of the conventional tags:
+//
+// - orig :: means the ADC-level frames out of the simulation
+// - gauss :: means the signal processing with Gaussian filter
+//
+// The file name may have a "%" formatter which will be interpolated
+// against the APA ID number.  If omitted, "-apa%d" will be inserted
+// at the end of the base file name just prior to the extention
+// (likely .npz).
 
 local wc = import "wirecell.jsonnet";
 local pg = import "pgraph.jsonnet";
@@ -26,59 +41,67 @@ local io = import "ioutils.jsonnet";
 local nf = import "nf.jsonnet";
 local sp = import "sp.jsonnet";
 
-function(input, output, wires, resps, noisef=null, app='Pgrapher') 
-local seeds = [0,1,2,3,4];  // maybe let CLI set?
-local depos = io.npz_source_depo("depos", input);
-
 local params = import "pgrapher/experiment/pdsp/simparams.jsonnet";
 local spfilt = import "pgrapher/experiment/pdsp/sp-filters.jsonnet";
+local chndb = import "pdsp_chndb.jsonnet";
+
+function(input, taps, wires, resps, noisef=null, thread='single')
+    local app = if thread == 'single'
+                then 'Pgrapher'
+                else 'TbbFlow';
+    local seeds = [0,1,2,3,4];  // maybe let CLI set?
+    local depos = io.npz_source_depo("depos", input);
+
+
+    local wireobj = tz.wire_file(wires);
+    local anodes = tz.anodes(wireobj, params.det.volumes);
+
+    local apaids = std.range(0, std.length(anodes)-1);
+
+    local robjs = tz.responses(resps, params.elec, params.daq);
+
+    local random = tz.random(seeds);
+
+    local drifter = tz.drifter(params.det.volumes, params.lar, random);
+    local bagger = tz.bagger(params.daq);
+
+    local chndb_perfect(n) =
+        chndb.perfect(anodes[n], robjs.fr,
+                      params.daq.nticks,
+                      params.daq.tick);
+
+    local tap_out(tap, apaid) =
+        if std.objectHas(taps, tap)
+        then [io.frame_out(tap+"%d", apaid, taps[tap], tags=[tap+"%d"], cap = tap=="gauss")]
+        else [];
+
+    local sim(n) = [
+        local anode = anodes[n];
+        tz.sim(anode,               // kitchen
+               robjs.pirs,          // sink
+               params.daq,
+               params.adc,
+               params.lar,
+               noisef,
+               'adc',
+               random)
+    ] + tap_out("orig", n);
+
+    local adcpermv = tz.adcpermv(params.adc);
+    local nfsp(n) = [
+        nf(anodes[n], robjs.fr, chndb_perfect(n),
+           params.daq.nticks, params.daq.tick),
+    ] + tap_out("raw", n) + [
+        sp(anodes[n], robjs.fr, robjs.er, spfilt, adcpermv)
+    ] + tap_out("gauss", n);
+
+    local oneapa(n) = pg.pipeline(sim(n) + nfsp(n));
+
+    local pipes = [oneapa(n) for n in apaids];
+
+    local body = pg.fan.fanout('DepoSetFanout', pipes);
+    local full = pg.pipeline([depos, drifter, bagger, body]);
+
+    tz.main(full, app)
 
-local wireobj = tz.wire_file(wires);
-local anodes = tz.anodes(wireobj, params.det.volumes);
-
-local apaids = std.range(0, std.length(anodes)-1);
-
-local robjs = tz.responses(resps, params.elec, params.daq);
-
-local random = tz.random(seeds);
-
-local drifter = tz.drifter(params.det.volumes, params.lar, random);
-local bagger = tz.bagger(params.daq);
-
-local sim(n) =
-    tz.sim(anodes[n], robjs.pirs, 
-           params.daq, params.adc, params.lar,
-           noisef, 'adc', random);
-
-local adcpermv = tz.adcpermv(params.adc);
-local nfsp(n) =
-    pg.pipeline([
-        //nf(anodes[n], robjs.fr, params.daq.nticks, params.daq.tick),
-        sp(anodes[n], robjs.fr, robjs.er, spfilt, adcpermv)]);
-
-local outfile(n) = {
-    local l = std.split(output,"."),
-    ret:"%s-apa%d.%s"%[l[0],n,l[1]]
-}.ret;
-local oneapa(n) = {
-    local name = "gauss%d"%n,
-    local outf = outfile(n),
-    pipe: pg.pipeline([
-        sim(n), nfsp(n),
-        io.frame_save_npz(name, outf, digitize=false, tags=[name]),
-        io.frame_sink(name)])
-}.pipe;
-
-local pipes = [oneapa(n) for n in apaids];
-
-// local frame_tags = ["gauss%d"%n for n in apaids];
-// local frames = io.frame_save_npz("frames", output,
-//                                  digitize = false, tags=frame_tags);
-// local dump = io.frame_sink();
-// local body = pg.fan.pipe('DepoSetFanout', pipes, 'FrameFanin',
-//                          outtags=frame_tags);
-
-local body = pg.fan.fanout('DepoSetFanout', pipes);
-local full = pg.pipeline([depos, drifter, bagger, body]);
-tz.main(full, app)
 
diff --git a/cfg/main-depos-sim.jsonnet b/cfg/main-depos-sim.jsonnet
new file mode 100644
index 0000000..e3a9df4
--- /dev/null
+++ b/cfg/main-depos-sim.jsonnet
@@ -0,0 +1,63 @@
+// This is a main wire-cell configuration file.
+//
+// It implements the chain (depos)->[sim[+noise]]->(Voltage|ADC).
+//
+// It takes a number of top-level-arguments (TLA).
+//
+// Run like
+//
+//  wire-cell \
+//    -A input=depos.npz -A output=frames.npz \
+//    -A wires=wires-geometry.json.bz2 \
+//    -A resps=field-response.json.bz2 \
+//    -A noisef=/path/to/noise/model/file \
+//    -A tier=[adc|voltage] \
+//    -A app=[Pgrapher|TbbFlow] \
+//    -c main-depos-sim-adc.jsonnet
+//
+// The 'noisef' TLA is optional and specifies a noise model.  If not
+// given, only signal is simulated.
+//
+// The 'tier' is optional and default to 'adc'.  If 'voltage' is
+// given, the output frame will not have the ADC model applied and
+// will be in units of Volts instead of ADC counts.
+
+local wc = import "wirecell.jsonnet";
+local pg = import "pgraph.jsonnet";
+
+local tz = import "toyzero.jsonnet";
+local io = import "ioutils.jsonnet";
+
+function(input, output, wires, resps, noisef=null, tier='adc', app='Pgrapher') 
+local seeds = [0,1,2,3,4];  // maybe let CLI set?
+local depos = io.npz_source_depo("depos", input);
+
+local params = tz.protodune_params;
+
+local wireobj = tz.wire_file(wires);
+local anodes = tz.anodes(wireobj, params.det.volumes);
+
+local apaids = std.range(0, std.length(anodes)-1);
+
+local pirs = tz.pirs(resps, params.daq, params.elec);
+
+local random = tz.random(seeds);
+
+local drifter = tz.drifter(params.det.volumes, params.lar, random);
+local bagger = tz.bagger(params.daq);
+
+local apasim(n) =
+    tz.apasim(anodes[n], pirs, 
+              params.daq, params.adc, params.lar,
+              noisef, tier, random);
+
+local simpipes = [apasim(n) for n in apaids];
+
+
+local frames = io.frame_save_npz("frames", output, digitize = tier=='adc');
+local dump = io.frame_sink();
+
+local simbody = pg.fan.pipe('DepoSetFanout', simpipes, 'FrameFanin');
+local full = pg.pipeline([depos, drifter, bagger, simbody, frames, dump]);
+tz.main(full, app)
+
diff --git a/cfg/nf.jsonnet b/cfg/nf.jsonnet
index 7a10551..ce107b8 100644
--- a/cfg/nf.jsonnet
+++ b/cfg/nf.jsonnet
@@ -6,102 +6,9 @@
 local wc = import "wirecell.jsonnet";
 local pg = import "pgraph.jsonnet";
 
-function(anode, fieldresp, nsamples, tick=0.5*wc.us, rms_cuts=[]) {
+function(anode, fieldresp, chndb, nsamples, tick=0.5*wc.us, rms_cuts=[]) {
     local apaid = anode.data.ident,
 
-    local chndb = {
-        type: 'OmniChannelNoiseDB',
-        name: 'ocndbperfect%d' % apaid,
-        uses: [anode, fieldresp],
-        data: {
-            anode: wc.tn(anode),
-            field_response: wc.tn(fieldresp),
-            tick: tick,
-
-            // This sets the number of frequency-domain bins used in the noise
-            // filtering.  It is not necessarily true that the time-domain
-            // waveforms have the same number of ticks.  This must be non-zero.
-            nsamples: nsamples,
-
-            // Group channels into their domains of coherency
-            groups: [
-                std.range(apaid * 2560 + u * 40, apaid * 2560 + (u + 1) * 40 - 1)
-                for u in std.range(0, 19)
-            ] + [
-                std.range(apaid * 2560 + 800 + v * 40, apaid * 2560 + 800 + (v + 1) * 40 - 1)
-                for v in std.range(0, 19)
-            ] + [
-                std.range(apaid * 2560 + 1600 + w * 48, apaid * 2560 + 1600 + (w + 1) * 48 - 1)
-                for w in std.range(0, 19)
-            ],
-
-
-            // Overide defaults for specific channels.  If an info is
-            // mentioned for a particular channel in multiple objects in this
-            // list then last mention wins.
-            channel_info: [
-                // First entry provides default channel info across ALL
-                // channels.  Subsequent entries override a subset of channels
-                // with a subset of these entries.  There's no reason to
-                // repeat values found here in subsequent entries unless you
-                // wish to change them.
-                {
-                    channels: std.range(apaid * 2560, (apaid + 1) * 2560 - 1),
-                    nominal_baseline: 2048.0,  // adc count
-                    gain_correction: 1.0,  // unitless
-                    response_offset: 0.0,  // ticks?
-                    pad_window_front: 10,  // ticks?
-                    pad_window_back: 10,  // ticks?
-                    decon_limit: 0.02,
-                    decon_limit1: 0.09,
-                    adc_limit: 15,
-                    roi_min_max_ratio: 0.8, // default 0.8
-                    min_rms_cut: 1.0,  // units???
-                    max_rms_cut: 30.0,  // units???
-
-                    // parameter used to make "rcrc" spectrum
-                    rcrc: 1.1 * wc.millisecond, // 1.1 for collection, 3.3 for induction
-                    rc_layers: 1, // default 2
-
-                    // parameters used to make "config" spectrum
-                    reconfig: {},
-
-                    // list to make "noise" spectrum mask
-                    freqmasks: [],
-
-                    // field response waveform to make "response" spectrum.
-                    response: {},
-                },
-                {
-                    //channels: { wpid: wc.WirePlaneId(wc.Ulayer) },
-                    channels: std.range(apaid * 2560, apaid * 2560 + 800- 1),
-                    response: { wpid: wc.WirePlaneId(wc.Ulayer) },
-                    response_offset: 120, // offset of the negative peak
-                    pad_window_front: 20,
-                    decon_limit: 0.02,
-                    decon_limit1: 0.07,
-                    roi_min_max_ratio: 3.0,
-                },
-                {
-                    //channels: { wpid: wc.WirePlaneId(wc.Vlayer) },
-                    channels: std.range(apaid * 2560 + 800, apaid * 2560 + 1600- 1),
-                    response: { wpid: wc.WirePlaneId(wc.Vlayer) },
-                    response_offset: 124,
-                    decon_limit: 0.01,
-                    decon_limit1: 0.08,
-                    roi_min_max_ratio: 1.5,
-                },
-                {
-                    //channels: { wpid: wc.WirePlaneId(wc.Wlayer) },
-                    channels: std.range(apaid * 2560 + 1600, apaid * 2560 + 2560- 1),
-                    nominal_baseline: 400.0,
-                    decon_limit: 0.05,
-                    decon_limit1: 0.08,
-                },
-            ] + rms_cuts,
-        },                      // data
-    },                          // chndb
-
     local single = {
         type: 'pdOneChannelNoise',
         name: 'ocn%d'%apaid,
@@ -109,9 +16,6 @@ function(anode, fieldresp, nsamples, tick=0.5*wc.us, rms_cuts=[]) {
             noisedb: wc.tn(chndb),
             anode: wc.tn(anode),
             resmp: [
-                {channels: std.range(2128, 2175), sample_from: 5996},
-                {channels: std.range(1520, 1559), sample_from: 5996},
-                {channels: std.range( 440,  479), sample_from: 5996},
             ],
         },
     },
@@ -126,7 +30,6 @@ function(anode, fieldresp, nsamples, tick=0.5*wc.us, rms_cuts=[]) {
 
     local obnf = pg.pnode({
 
-
         type: 'OmnibusNoiseFilter',
         name: 'nf%d'%apaid,
         data: {
diff --git a/cfg/pdsp_chndb.jsonnet b/cfg/pdsp_chndb.jsonnet
new file mode 100644
index 0000000..5a3bda8
--- /dev/null
+++ b/cfg/pdsp_chndb.jsonnet
@@ -0,0 +1,106 @@
+// This defines channel noise databases for noise filtering for pdsp.
+
+local wc = import "wirecell.jsonnet";
+
+{
+    // The "perfect noise" database is one that is free of any
+    // "special" considerations such as per channel variability.  The
+    // "official" perfect chndb depends on the official "chndb-base"
+    // and that seems to be adulterated with specific settings.  We
+    // try to start fresh here.
+    perfect(anode, fr, nsamples, tick=0.5*wc.us) :: {
+        local apaid = anode.data.ident,
+        type:'OmniChannelNoiseDB',
+        name: 'ocndbperfect-%s' % anode.name,
+        uses: [anode, fr],
+        data: {
+            anode: wc.tn(anode),
+            field_response: wc.tn(fr),
+            tick: tick,
+            nsamples: nsamples,
+
+            groups: [
+                std.range(apaid * 2560 + u * 40, apaid * 2560 + (u + 1) * 40 - 1)
+                for u in std.range(0, 19)
+            ] + [
+                std.range(apaid * 2560 + 800 + v * 40, apaid * 2560 + 800 + (v + 1) * 40 - 1)
+                for v in std.range(0, 19)
+            ] + [
+                std.range(apaid * 2560 + 1600 + w * 48, apaid * 2560 + 1600 + (w + 1) * 48 - 1)
+                for w in std.range(0, 19)
+            ],
+            
+            // last match wins
+            channel_info: [
+
+                // First entry provides default channel info across ALL
+                // channels.  Subsequent entries override a subset of channels
+                // with a subset of these entries.  There's no reason to
+                // repeat values found here in subsequent entries unless you
+                // wish to change them.
+                {
+                    channels: std.range(apaid * 2560, (apaid + 1) * 2560 - 1),
+                    nominal_baseline: 2350.0,  // adc count
+                    gain_correction: 1.0,  // unitless
+                    response_offset: 0.0,  // ticks?
+                    pad_window_front: 10,  // ticks?
+                    pad_window_back: 10,  // ticks?
+                    decon_limit: 0.02,
+                    decon_limit1: 0.09,
+                    adc_limit: 15,
+                    roi_min_max_ratio: 0.8, // default 0.8
+                    min_rms_cut: 1.0,  // units???
+                    max_rms_cut: 30.0,  // units???
+
+                    // parameter used to make "rcrc" spectrum
+                    rcrc: 1.1 * wc.millisecond, // 1.1 for collection, 3.3 for induction
+                    rc_layers: 1, // default 2
+
+                    // parameters used to make "config" spectrum
+                    reconfig: {},
+
+                    // list to make "noise" spectrum mask
+                    freqmasks: [],
+
+                    // field response waveform to make "response" spectrum.
+                    response: {},
+
+                },
+
+                {
+                    //channels: { wpid: wc.WirePlaneId(wc.Ulayer) },
+	            channels: std.range(apaid * 2560, apaid * 2560 + 800- 1),
+                    /// this will use an average calculated from the anode
+                    // response: { wpid: wc.WirePlaneId(wc.Ulayer) },
+                    /// this uses hard-coded waveform.
+                    response_offset: 120, // offset of the negative peak
+                    pad_window_front: 20,
+                    decon_limit: 0.02,
+                    decon_limit1: 0.07,
+                    roi_min_max_ratio: 3.0,
+                },
+
+                {
+                    //channels: { wpid: wc.WirePlaneId(wc.Vlayer) },
+	            channels: std.range(apaid * 2560 + 800, apaid * 2560 + 1600- 1),
+                    /// this will use an average calculated from the anode
+                    // response: { wpid: wc.WirePlaneId(wc.Vlayer) },
+                    /// this uses hard-coded waveform.
+                    decon_limit: 0.01,
+                    decon_limit1: 0.08,
+                    roi_min_max_ratio: 1.5,
+                },
+
+                {
+                    //channels: { wpid: wc.WirePlaneId(wc.Wlayer) },
+	            channels: std.range(apaid * 2560 + 1600, apaid * 2560 + 2560- 1),
+                    nominal_baseline: 900.0,
+                    decon_limit: 0.05,
+                    decon_limit1: 0.08,
+                },
+
+
+            ],
+        }                       // data
+    }                           // perfect()
+}
diff --git a/cfg/sp.jsonnet b/cfg/sp.jsonnet
index a5928e4..1c8d9c5 100644
--- a/cfg/sp.jsonnet
+++ b/cfg/sp.jsonnet
@@ -75,7 +75,6 @@ function(anode, fieldresp, elecresp, spfilt, adcpermv, perchan=null) {
             mp2_roi_tag: 'mp2_roi%d' % apaid,
             
             isWrapped: false,
-            sparse: false,
             // process_planes: [0, 2],
         }
     }, nin=1, nout=1, uses=[anode, fieldresp, elecresp] + pcuses + spfilt),
diff --git a/cfg/toyzero.jsonnet b/cfg/toyzero.jsonnet
index 4445cd1..21493fa 100644
--- a/cfg/toyzero.jsonnet
+++ b/cfg/toyzero.jsonnet
@@ -116,7 +116,7 @@ local pg = import "pgraph.jsonnet";
     
 
     // A per anode configure node for simulating noise.
-    noisesim(anode, noisef, daq, csdb=null, rnd=$.random()) : {
+    noisesim(anode, noisef, daq, chstat=null, rnd=$.random()) : {
         local apaid = anode.data.ident,
         
         local noise_model = {
@@ -124,13 +124,13 @@ local pg = import "pgraph.jsonnet";
             name: "emperical-noise-model-%d" % apaid,
             data: {
                 anode: wc.tn(anode),
-                chanstat: if std.type(csdb) == "null" then "" else wc.tn(csdb),
+                chanstat: if std.type(chstat) == "null" then "" else wc.tn(chstat),
                 spectra_file: noisef,
                 nsamples: daq.nticks,
                 period: daq.tick,
                 wire_length_scale: 1.0*wc.cm, // optimization binning
             },
-            uses: [anode] + if std.type(csdb) == "null" then [] else [csdb],
+            uses: [anode] + if std.type(chstat) == "null" then [] else [chstat],
         },
         ret: pg.pnode({
             type: "AddNoise",
@@ -204,21 +204,19 @@ local pg = import "pgraph.jsonnet";
     // The tier can be 'adc' or something else if no digitizer.
     sim(anode, pirs, daq, adc, lar, noisef=null, tier='adc', rnd=$.random()) : {
 
-        // fixme: make configurable
-        local csdb = null,
+        local apaid = anode.data.ident,
 
         local beg = if std.type(lar) == "null" || std.type(pirs) == "null" then [] else [
             $.sigsim(anode, pirs, daq, lar, rnd)],
 
         local mid = if std.type(noisef) == "null" then [] else [
-            $.noisesim(anode, noisef, daq, rnd, csdb)],
+            $.noisesim(anode, noisef, daq, rnd=rnd)],
 
         local end = if tier == 'adc' then [$.digisim(anode, adc)] else [],
 
         pipeline: pg.pipeline(beg + mid + end),
     }.pipeline,
 
-
     local plugins = [
         "WireCellSio", "WireCellAux",
         "WireCellGen", "WireCellSigProc",
diff --git a/cfg/utils.jsonnet b/cfg/utils.jsonnet
new file mode 100644
index 0000000..4441e63
--- /dev/null
+++ b/cfg/utils.jsonnet
@@ -0,0 +1,12 @@
+// fixme: many/all of these probably could get lifted to wct/cfg/
+
+{
+    // Return true if string s has at least one % symbol.
+    haspct(s, pct="%"):: std.length(std.findSubstr(pct, s))>0,
+
+    // append a suffix to the base name of a file name, prior to .ext
+    basename_append(filename, suffix) :: {
+        local l = std.split(filename, "."),
+        ret:"%s%s.%s"%[l[0], suffix, l[1]]
+    }.ret,
+}
diff --git a/dot.envrc b/dot.envrc
index 361e981..63d2db9 100644
--- a/dot.envrc
+++ b/dot.envrc
@@ -1,5 +1,6 @@
 load_prefix $HOME/dev/ls4gan/toyzero/wire-cell-toolkit/install
 path_add WIRECELL_PATH $HOME/dev/ls4gan/toyzero/wire-cell-toolkit/cfg
+path_add WIRECELL_PATH $HOME/dev/ls4gan/toyzero/wire-cell-data
 load_prefix $HOME/opt/jsonnet
 
 layout python3
diff --git a/testit.sh b/testit.sh
new file mode 100755
index 0000000..58df2a9
--- /dev/null
+++ b/testit.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+set -x
+
+tiers=(raw orig gauss threshold)
+
+taps=""
+for tier in ${tiers[*]}
+do
+    taps+="{\"$tier\":\"testit/fake-frames-${tier}.npz\"}"
+done
+
+if [ -f testit/fake-frames-orig-apa0.npz ] ; then
+    echo "wire-cell has run already, rm testit if you want"
+else
+    mkdir -p testit
+    wire-cell \
+        -l stdout -L debug -P cfg\
+        -A input=data/depos/depos.npz \
+        --tla-code taps=$taps \
+        -A wires=data/wires/wires.json.bz2  \
+        -A resps=data/resps/fake-resps.json.bz2 \
+        -A thread=multi \
+        -A noisef=protodune-noise-spectra-v1.json.bz2 \
+        -c cfg/main-depos-sigproc.jsonnet || exit 
+fi
+
+
+for tier in raw orig gauss
+do
+    for apaid in 0 1 2 3 4 5
+    do
+        tag=${tier}${apaid}
+        wirecell-gen \
+            plot-sim \
+            testit/fake-frames-${tier}-apa${apaid}.npz \
+            -p frames -b 0,2560 --tag ${tier}${apaid} \
+            testit/fake-frames-${tier}-apa${apaid}.png
+    done
+done
+
+
+

From aad34192571869939c4bfff71af9b2b116dccbe3 Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Fri, 23 Jul 2021 16:35:26 -0400
Subject: [PATCH 05/15] Checkpoint

---
 Snakefile | 36 ++++++++++++++++++++----------------
 testit.sh | 23 ++++++++++++++++++-----
 2 files changed, 38 insertions(+), 21 deletions(-)

diff --git a/Snakefile b/Snakefile
index 0fb5631..6a87de3 100644
--- a/Snakefile
+++ b/Snakefile
@@ -128,24 +128,28 @@ rule all_wires:
 def gen_depos_cfg(w):
     'Dig out the bounding box of the detector'
 
-    params_cmd = 'wcsonnet pgrapher/experiment/pdsp/simparams.jsonnet'
-    jtext = subprocess.check_output(params_cmd, shell=True)
-    jdat = json.loads(jtext)
-    bb = jdat['det']['bounds']
-
-    p1 = bb['tail']
-    p2 = bb['head']
-    corn = list()
-    diag = list()
-    for l in "xyz":
-        c = p1[l]
-        dc = p2[l]-p1[l]
-        # warning, pretend we know WCT's SoU here....
-        corn.append(f'{c:.1f}*mm')
-        diag.append(f'{dc:.1f}*mm')
+    # params_cmd = 'wcsonnet pgrapher/experiment/pdsp/simparams.jsonnet'
+    # jtext = subprocess.check_output(params_cmd, shell=True)
+    # jdat = json.loads(jtext)
+    # bb = jdat['det']['bounds']
+    # p1 = bb['tail']
+    # p2 = bb['head']
+    # corn = list()
+    # diag = list()
+    # for l in "xyz":
+    #     c = p1[l]
+    #     dc = p2[l]-p1[l]
+    #     # warning, pretend we know WCT's SoU here....
+    #     corn.append(f'{c:.1f}*mm')
+    #     diag.append(f'{dc:.1f}*mm')
+
+    # found by running once and looking at AnodePlane log msgs
+    diag = '16000.0*mm,6100.0*mm,7000.0*mm'
+    corn = '-8000.0*mm,0.0*mm,0.0*mm'
 
     return dict(tracks = ntracks, sets = nevents, seed = seed,
-                corn = ','.join(corn), diag = ','.join(diag))
+                corn = corn, diag = diag)
+                #corn = ','.join(corn), diag = ','.join(diag))
 
 rule gen_depos:
     input:
diff --git a/testit.sh b/testit.sh
index 58df2a9..fb8b398 100755
--- a/testit.sh
+++ b/testit.sh
@@ -2,7 +2,9 @@
 
 set -x
 
-tiers=(raw orig gauss threshold)
+mkdir -p testit
+
+tiers=(orig gauss)
 
 taps=""
 for tier in ${tiers[*]}
@@ -10,13 +12,24 @@ do
     taps+="{\"$tier\":\"testit/fake-frames-${tier}.npz\"}"
 done
 
+if [ -f testit/depos.npz ] ; then
+    echo "depos already generated"
+else
+    wirecell-gen depo-lines \
+    --seed 1234 \
+    --tracks 100 \
+    --sets 1 \
+    --diagonal '16000.0*mm,6100.0*mm, 7000.0*mm' \
+    --corner   '-8000.0*mm,0.0*mm,0.0*mm' \
+    --output testit/depos.npz || exit
+fi
+
 if [ -f testit/fake-frames-orig-apa0.npz ] ; then
     echo "wire-cell has run already, rm testit if you want"
 else
-    mkdir -p testit
     wire-cell \
         -l stdout -L debug -P cfg\
-        -A input=data/depos/depos.npz \
+        -A input=depos.npz \
         --tla-code taps=$taps \
         -A wires=data/wires/wires.json.bz2  \
         -A resps=data/resps/fake-resps.json.bz2 \
@@ -26,7 +39,7 @@ else
 fi
 
 
-for tier in raw orig gauss
+for tier in orig gauss
 do
     for apaid in 0 1 2 3 4 5
     do
@@ -35,7 +48,7 @@ do
             plot-sim \
             testit/fake-frames-${tier}-apa${apaid}.npz \
             -p frames -b 0,2560 --tag ${tier}${apaid} \
-            testit/fake-frames-${tier}-apa${apaid}.png
+            testit/fake-frames-${tier}-apa${apaid}.png || exit
     done
 done
 

From f5d3b093bbf9ff5c80d33fdeb809ef134f7146fb Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Mon, 26 Jul 2021 17:55:25 -0400
Subject: [PATCH 06/15] Almost there to making full chain

---
 Snakefile | 168 ++++++++++++++++++++++++++----------------------------
 testit.sh |   4 +-
 2 files changed, 83 insertions(+), 89 deletions(-)

diff --git a/Snakefile b/Snakefile
index 6a87de3..aa9acaa 100644
--- a/Snakefile
+++ b/Snakefile
@@ -23,12 +23,10 @@ ntracks = config.get("ntracks", 10)
 nevents = config.get("nevents", 10)
 wcloglvl = config.get("wcloglvl", "info")
 
-tiers = config.get("tiers", ["noiseless"])
-
-# print(f"OUTDIR:{outdir}")
-# print(f"NEVENTS:{nevents}")
-# print(f"WCLOGLVL:{wcloglvl}")
-print(f"TIERS:{tiers}, {type(tiers)}")
+# limit number of threads per wire-cell job
+threads = config.get("threads", 1)
+# single threaded uses Pgrapher, multi uses TbbFlow
+threading = "single" if threads == 1 else "multi"
 
 # The rest are hard wired for now
 wcdata_url = "https://github.com/WireCell/wire-cell-data/raw/master"
@@ -49,8 +47,10 @@ apa_iota = list(range(6))
 # associated with a particular detector response.
 DOMAINS = ["fake", "real"]
 
-# The data tiers for frame or image
-TIERS = ["noiseless", "signal"]
+# The data tiers for frame or image. We make all tiers in one job.
+# The 'orig' is the output of the simulation and 'gauss' is the output
+# of signal processing using the charge-preserving filters.
+TIERS = ["orig", "gauss"]
 
 # some important file names
 real_resps    = f'{datadir}/resps/real-resps.{wcdata_ext}'
@@ -58,6 +58,7 @@ fake_resps    = f'{datadir}/resps/fake-resps.{wcdata_ext}'
 domain_resps  = f'{datadir}/resps/{{domain}}-resps.{wcdata_ext}'
 wires_file    = f'{datadir}/wires/wires.{wcdata_ext}'
 depos_file    = f'{datadir}/depos/depos.npz'
+noise_file    = f'{datadir}/noise/protodune-noise-spectra-v1.{wcdata_ext}'
 
 # resp - prepare response files
 
@@ -79,6 +80,15 @@ rule gen_resp_fake:
     wirecell-sigproc frzero -n 0 -o {output} {input}
     '''
 
+rule get_noisef:
+    input:
+        HTTP.remote(f'{wcdata_url}/protodune-noise-spectra-v1.{wcdata_ext}', keep_local=True)
+    output:
+        temp(noise_file)
+    run:
+        shell("mkdir -p {datadir}")
+        shell("cp {input} {output}")
+
 rule plot_resp:
     input:
         domain_resps
@@ -125,44 +135,19 @@ rule all_wires:
 
 # depos - generate ionization point depositions
 
-def gen_depos_cfg(w):
-    'Dig out the bounding box of the detector'
-
-    # params_cmd = 'wcsonnet pgrapher/experiment/pdsp/simparams.jsonnet'
-    # jtext = subprocess.check_output(params_cmd, shell=True)
-    # jdat = json.loads(jtext)
-    # bb = jdat['det']['bounds']
-    # p1 = bb['tail']
-    # p2 = bb['head']
-    # corn = list()
-    # diag = list()
-    # for l in "xyz":
-    #     c = p1[l]
-    #     dc = p2[l]-p1[l]
-    #     # warning, pretend we know WCT's SoU here....
-    #     corn.append(f'{c:.1f}*mm')
-    #     diag.append(f'{dc:.1f}*mm')
-
-    # found by running once and looking at AnodePlane log msgs
-    diag = '16000.0*mm,6100.0*mm,7000.0*mm'
-    corn = '-8000.0*mm,0.0*mm,0.0*mm'
-
-    return dict(tracks = ntracks, sets = nevents, seed = seed,
-                corn = corn, diag = diag)
-                #corn = ','.join(corn), diag = ','.join(diag))
-
 rule gen_depos:
     input:
         wires_file
     params:
-        p = gen_depos_cfg
+        diag = '16000.0*mm,6100.0*mm,7000.0*mm',
+        corn = '-8000.0*mm,0.0*mm,0.0*mm'
     output:
         temp(depos_file)
     shell: '''
     wirecell-gen depo-lines \
-    --seed {params.p[seed]} \
-    --tracks {params.p[tracks]} --sets {params.p[sets]} \
-    --diagonal '{params.p[diag]}' --corner '{params.p[corn]}' \
+    --seed {seed} \
+    --tracks {tracks} --sets {sets} \
+    --diagonal '{diag}' --corner '{corn}' \
     --output {output}
     '''
 
@@ -183,24 +168,20 @@ rule all_depos:
 
 # frames
 
-def wct_cfg_file(w):
-    slugs = dict(signal="depos-sigproc",
-                 noiseless="depos-sim-adc")
-    slug = slugs[w.tier]
-    return f'cfg/main-{slug}.jsonnet'
+wct_cfg_file = 'cfg/main-sigproc.jsonnet'
 
-
-# note, passes bogus TLAs so don't use the genearted json!
+# note, we pass bogus TLAs so don't use the generated json for
+# anything real!
 rule wct_dots:
     input:
         config = wct_cfg_file
     output:
-        json = temp(f'{plotdir}/dots/{{tier}}/cfg.json'),
-        dot  = temp(f'{plotdir}/dots/{{tier}}/dag.dot'),
-        png  = f'{plotdir}/dots/{{tier}}/dag.png',
-        pdf  = f'{plotdir}/dots/{{tier}}/dag.pdf'
+        json = temp(f'{plotdir}/dots/cfg.json'),
+        dot  = temp(f'{plotdir}/dots/dag.dot'),
+        png  = f'{plotdir}/dots/dag.png',
+        pdf  = f'{plotdir}/dots/dag.pdf'
     shell: '''
-    mkdir -p {plotdir}/dots/{wildcards.tier};
+    mkdir -p {plotdir}/dots;
     wcsonnet \
     -P cfg \
     -A input=DEPOS-FILE \
@@ -214,50 +195,59 @@ rule wct_dots:
     '''
 rule all_dots:
     input:
-        expand(rules.wct_dots.output, tier=tiers)
+        rules.wct_dots.output
 
 # this gives the pattern for one per-APA frame file.  The %d is
 # interpolated by wire-cell configuration.
-frames_pattern = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa%d.npz'
+
 frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.npz'
 
 def frame_taps(w):
-    if w.tier == "noiseless":
-        tap = "orig"
-    else:
-        tap = "gauss"
-    fp = frames_pattern.format(**dict(w))
-    return dict(tap=tap, pat=fp)
+    frames_pattern = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa%d.npz'
+    taps = list()
+    for tier in ('orig', 'gauss'):
+        d = dict(w)
+        d["tier"] = tier
+        taps.append('"%s":"%s"' % (tier, frames_pattern.format(**d)))
+
+    taps = ",".join(taps)
+    return '{%s}'%taps
+
+def frame_files():
+    frames_pattern = datadir + '/frames/{tier}/{{domain}}-frames-apa{apaid}.npz'
+    return expand(frames_pattern, tier=TIERS, apaid = apa_iota)
 
 rule sim_frames:
     input:
         wires = wires_file,
         resps = domain_resps,
         depos = depos_file,
-        config = wct_cfg_file
+        config = wct_cfg_file,
+        noise = noise_file
     output:
-        temp([frames_pattern%n for n in apa_iota])
+        frame_files()
     params:
-        p = frame_taps
+        taps = frame_taps
     shell: '''
     rm -f {output}; 
+    mkdir -p {datadir}/frames/orig {datadir}/frames/gauss
     wire-cell \
+    --threads 4 \
+    -A thread={threading} \
     -l stdout -L {config[wcloglvl]} \
     -P cfg \
     -A input={input.depos} \
-    --tla-code 'taps={{"{params.p[tap]}":"{params.p[pat]}"}}' \
+    --tla-code 'taps={params.taps}' \
     -A wires={input.wires} \
     -A resps={input.resps} \
+    -A noisef={input.noise} \
     -c {input.config}
     '''
         
 def gen_plot_frames(w):
     i = int(w.apa)
-    if w.tier == "noiseless":
-        return dict(chb=f'{i},{i+2560}', tag="")
-    if w.tier == "signal":
-        tag = f"gauss{i}"
-        return dict(chb=f'0,2560', tag=tag)
+    tag = f"{w.tier}{i}"
+    return dict(chb=f'0,2560', tag=tag)
 
 rule plot_frames:
     input:
@@ -284,13 +274,15 @@ rule plot_frames_hidpi:
 
 rule all_frames:
     input:
-        expand(rules.sim_frames.output, domain=["real","fake"],
-               tier=tiers),
+        rules.all_resp.input,
+        rules.all_wires.input,
+        rules.all_depos.input,
+        expand(rules.sim_frames.output, domain=["real","fake"]),
         expand(rules.plot_frames.output, domain=["real","fake"],
-               tier=tiers,
+               tier=TIERS,
                ext=["png","pdf"], apa=apa_iota),
         expand(rules.plot_frames_hidpi.output, domain=["real","fake"],
-               tier=tiers, apa=[0])
+               tier=TIERS, apa=[0])
 
 
 
@@ -305,21 +297,21 @@ rule all_frames:
 ## static data (ie, defined right here).  So, that is what we do.
 #
 split_outer_product = dict(
-#    domain = ["protodune"],
     event  = list(range(nevents)),
-    apa    = apa_iota,
     plane  = ["U","V","W"],
 )
 
+# frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.npz'
+
 rule split_images:
     input:
         frames_wildcard
     output:
-        expand(datadir+'/images/{{tier}}/{{domain}}/protodune-orig-{event}-{apa}-{plane}.npz',
+        expand(datadir+'/images/{{tier}}/{{domain}}/protodune-{{tier}}{{apa}}-{event}-{plane}.npz',
                **split_outer_product)
     shell: '''
     wirecell-util frame-split \
-    -f {datadir}/images/{wildcards.tier}/{wildcards.domain}/{{detector}}-{{tag}}-{{index}}-{{anodeid}}-{{planeletter}}.npz \
+    -f {datadir}/images/{wildcards.tier}/{wildcards.domain}/{{detector}}-{{tag}}-{{index}}-{{planeletter}}.npz \
     {input}
     '''
 
@@ -335,9 +327,9 @@ def gen_title(w):
 ## Above is 1->N, here is 1->1.
 rule plot_split_images:
     input:
-        datadir+'/images/{tier}/{domain}/protodune-orig-{event}-{apa}-{plane}.npz',
+        datadir+'/images/{tier}/{domain}/protodune-{tier}{apa}-{event}-{plane}.npz',
     output:
-        plotdir+'/images/{tier}/{domain}/{cmap}/protodune-orig-{event}-{apa}-{plane}.{ext}'
+        plotdir+'/images/{tier}/{domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}.{ext}'
     params:
         title = gen_title
     shell: '''
@@ -349,25 +341,27 @@ rule plot_split_images:
     --zoom 300:500,0:1000 --mask 0 --vmin -50 --vmax 50 \
     --dpi 600 --baseline=median -o {output} {input}
     '''
+
+rule just_images:
+    input:
+        rules.all_frames.input,
+        expand(rules.split_images.output,
+               domain=["real","fake"],
+               tier=TIERS, apa=apa_iota)
+
 ## note, list-of-list for the split_images rule
 rule all_images:
     input:
-        expand(rules.split_images.output,
-               domain=["real","fake"], tier=tiers),
+        rules.just_images.input,
         expand(
             rules.plot_split_images.output,
             domain = ["real","fake"],
-            tier = tiers,
-            event  = [0], apa=[2], plane=["U"],
+            tier = TIERS,
+            event  = [0], apa=[0], plane=["U","V","W"],
             ext    = ["png", "pdf", "svg"],
-            cmap   = ["seismic", "Spectral", "terrain", "coolwarm", "viridis"],
+            cmap   = ["seismic", "viridis"],
         )
 
-rule just_images:
-    input:
-        expand(rules.split_images.output,
-               domain=["real","fake"],
-               tier=tiers)
 
 rule all:
     input:
diff --git a/testit.sh b/testit.sh
index fb8b398..e4ff9fe 100755
--- a/testit.sh
+++ b/testit.sh
@@ -19,7 +19,7 @@ else
     --seed 1234 \
     --tracks 100 \
     --sets 1 \
-    --diagonal '16000.0*mm,6100.0*mm, 7000.0*mm' \
+    --diagonal '16000.0*mm,6100.0*mm,7000.0*mm' \
     --corner   '-8000.0*mm,0.0*mm,0.0*mm' \
     --output testit/depos.npz || exit
 fi
@@ -29,7 +29,7 @@ if [ -f testit/fake-frames-orig-apa0.npz ] ; then
 else
     wire-cell \
         -l stdout -L debug -P cfg\
-        -A input=depos.npz \
+        -A input=testit/depos.npz \
         --tla-code taps=$taps \
         -A wires=data/wires/wires.json.bz2  \
         -A resps=data/resps/fake-resps.json.bz2 \

From 7e1606e8cabe5c7d1f09858b7c06b3e87464ca23 Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Tue, 27 Jul 2021 13:08:31 -0400
Subject: [PATCH 07/15] Variable name typo fixes

---
 Snakefile | 6 +++---
 dot.envrc | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/Snakefile b/Snakefile
index aa9acaa..b9785f4 100644
--- a/Snakefile
+++ b/Snakefile
@@ -146,8 +146,8 @@ rule gen_depos:
     shell: '''
     wirecell-gen depo-lines \
     --seed {seed} \
-    --tracks {tracks} --sets {sets} \
-    --diagonal '{diag}' --corner '{corn}' \
+    --tracks {ntracks} --sets {nevents} \
+    --diagonal '{params.diag}' --corner '{params.corn}' \
     --output {output}
     '''
 
@@ -168,7 +168,7 @@ rule all_depos:
 
 # frames
 
-wct_cfg_file = 'cfg/main-sigproc.jsonnet'
+wct_cfg_file = 'cfg/main-depos-sigproc.jsonnet'
 
 # note, we pass bogus TLAs so don't use the generated json for
 # anything real!
diff --git a/dot.envrc b/dot.envrc
index 63d2db9..1798950 100644
--- a/dot.envrc
+++ b/dot.envrc
@@ -1,6 +1,6 @@
-load_prefix $HOME/dev/ls4gan/toyzero/wire-cell-toolkit/install
-path_add WIRECELL_PATH $HOME/dev/ls4gan/toyzero/wire-cell-toolkit/cfg
-path_add WIRECELL_PATH $HOME/dev/ls4gan/toyzero/wire-cell-data
+load_prefix $HOME/wrk/ls4gan/toyzero/wire-cell-toolkit/install
+path_add WIRECELL_PATH $HOME/wrk/ls4gan/toyzero/wire-cell-toolkit/cfg
+path_add WIRECELL_PATH $HOME/wrk/ls4gan/toyzero/wire-cell-data
 load_prefix $HOME/opt/jsonnet
 
 layout python3

From 890dfc55f83a3e9a8f48115db4eb9675361c270c Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Wed, 28 Jul 2021 18:13:53 -0400
Subject: [PATCH 08/15] Allow different FRs for sim and sigproc

---
 Snakefile                      | 28 +++++++----
 cfg/main-depos-sigproc.jsonnet | 15 +++---
 cfg/toyzero.jsonnet            |  3 +-
 cfg/utils.jsonnet              | 11 +++++
 testit.sh                      | 85 ++++++++++++++++++----------------
 5 files changed, 85 insertions(+), 57 deletions(-)

diff --git a/Snakefile b/Snakefile
index b9785f4..a2e7881 100644
--- a/Snakefile
+++ b/Snakefile
@@ -185,9 +185,11 @@ rule wct_dots:
     wcsonnet \
     -P cfg \
     -A input=DEPOS-FILE \
-    --tla-code taps='{{"orig":"frame-orig-.npz","gauss":"frame-gauss.npz"}}' \
+    --tla-code taps='{{"orig":"frame-orig.npz","gauss":"frame-gauss.npz"}}' \
     -A wires=WIRES-FILE \
-    -A resps=RESPS-FILE \
+    -A resps_sim=RESPS-SIM-FILE \
+    -A resps_sigproc=RESPS-SIGPROC-FILE \
+    -A noisef=NOISE-FILE \
     {input.config} > {output.json};
     wirecell-pgraph dotify --no-params --jpath=-1 {output.json} {output.dot} ;
     dot -Tpng -o {output.png} {output.dot} ;
@@ -220,17 +222,19 @@ def frame_files():
 rule sim_frames:
     input:
         wires = wires_file,
-        resps = domain_resps,
+        resps_sim = domain_resps,
+        resps_sigproc = fake_resps,
         depos = depos_file,
         config = wct_cfg_file,
         noise = noise_file
     output:
-        frame_files()
+        temp(frame_files())
     params:
         taps = frame_taps
     shell: '''
     rm -f {output}; 
-    mkdir -p {datadir}/frames/orig {datadir}/frames/gauss
+    mkdir -p {datadir}/frames/orig;
+    mkdir -p {datadir}/frames/gauss;
     wire-cell \
     --threads 4 \
     -A thread={threading} \
@@ -239,7 +243,8 @@ rule sim_frames:
     -A input={input.depos} \
     --tla-code 'taps={params.taps}' \
     -A wires={input.wires} \
-    -A resps={input.resps} \
+    -A resps_sim={input.resps_sim} \
+    -A resps_sigproc={input.resps_sigproc} \
     -A noisef={input.noise} \
     -c {input.config}
     '''
@@ -272,12 +277,17 @@ rule plot_frames_hidpi:
     '''
 
 
+rule just_frames:
+    input:
+        expand(rules.sim_frames.output, domain=["real","fake"]),
+        
+
 rule all_frames:
     input:
         rules.all_resp.input,
         rules.all_wires.input,
         rules.all_depos.input,
-        expand(rules.sim_frames.output, domain=["real","fake"]),
+        rules.just_frames.input,
         expand(rules.plot_frames.output, domain=["real","fake"],
                tier=TIERS,
                ext=["png","pdf"], apa=apa_iota),
@@ -344,10 +354,10 @@ rule plot_split_images:
 
 rule just_images:
     input:
-        rules.all_frames.input,
+        rules.just_frames.input,
         expand(rules.split_images.output,
                domain=["real","fake"],
-               tier=TIERS, apa=apa_iota)
+               tier=["gauss"], apa=apa_iota)
 
 ## note, list-of-list for the split_images rule
 rule all_images:
diff --git a/cfg/main-depos-sigproc.jsonnet b/cfg/main-depos-sigproc.jsonnet
index f04e45d..78b9262 100644
--- a/cfg/main-depos-sigproc.jsonnet
+++ b/cfg/main-depos-sigproc.jsonnet
@@ -15,6 +15,8 @@
 //    -A taps={...see below...} \
 //    -A wires=wires-geometry.json.bz2 \
 //    -A resps=field-response.json.bz2 \
+//    -A resps_sim=field-response-for-sim.json.bz2 \
+//    -A resps_sigproc=field-response-for-sigproc.json.bz2 \
 //    -A noisef=/path/to/noise/model/file \
 //    -A thread=[single|multi] \
 //    -c main-depos-sim-adc.jsonnet
@@ -45,7 +47,7 @@ local params = import "pgrapher/experiment/pdsp/simparams.jsonnet";
 local spfilt = import "pgrapher/experiment/pdsp/sp-filters.jsonnet";
 local chndb = import "pdsp_chndb.jsonnet";
 
-function(input, taps, wires, resps, noisef=null, thread='single')
+function(input, taps, wires, resps_sim, resps_sigproc, noisef=null, thread='single')
     local app = if thread == 'single'
                 then 'Pgrapher'
                 else 'TbbFlow';
@@ -58,7 +60,8 @@ function(input, taps, wires, resps, noisef=null, thread='single')
 
     local apaids = std.range(0, std.length(anodes)-1);
 
-    local robjs = tz.responses(resps, params.elec, params.daq);
+    local robjs_sim = tz.responses(resps_sim, params.elec, params.daq);
+    local robjs_sigproc = tz.responses(resps_sigproc, params.elec, params.daq);
 
     local random = tz.random(seeds);
 
@@ -66,7 +69,7 @@ function(input, taps, wires, resps, noisef=null, thread='single')
     local bagger = tz.bagger(params.daq);
 
     local chndb_perfect(n) =
-        chndb.perfect(anodes[n], robjs.fr,
+        chndb.perfect(anodes[n], robjs_sim.fr,
                       params.daq.nticks,
                       params.daq.tick);
 
@@ -78,7 +81,7 @@ function(input, taps, wires, resps, noisef=null, thread='single')
     local sim(n) = [
         local anode = anodes[n];
         tz.sim(anode,               // kitchen
-               robjs.pirs,          // sink
+               robjs_sim.pirs,      // sink
                params.daq,
                params.adc,
                params.lar,
@@ -89,10 +92,10 @@ function(input, taps, wires, resps, noisef=null, thread='single')
 
     local adcpermv = tz.adcpermv(params.adc);
     local nfsp(n) = [
-        nf(anodes[n], robjs.fr, chndb_perfect(n),
+        nf(anodes[n], robjs_sigproc.fr, chndb_perfect(n),
            params.daq.nticks, params.daq.tick),
     ] + tap_out("raw", n) + [
-        sp(anodes[n], robjs.fr, robjs.er, spfilt, adcpermv)
+        sp(anodes[n], robjs_sigproc.fr, robjs_sigproc.er, spfilt, adcpermv)
     ] + tap_out("gauss", n);
 
     local oneapa(n) = pg.pipeline(sim(n) + nfsp(n));
diff --git a/cfg/toyzero.jsonnet b/cfg/toyzero.jsonnet
index 21493fa..35b2c88 100644
--- a/cfg/toyzero.jsonnet
+++ b/cfg/toyzero.jsonnet
@@ -1,6 +1,6 @@
 local wc = import "wirecell.jsonnet";
 local pg = import "pgraph.jsonnet";
-
+local ut = import "utils.jsonnet";
 
 // define general object for toyzero
 
@@ -26,6 +26,7 @@ local pg = import "pgraph.jsonnet";
 
     field_response(filename) :: {
         type: "FieldResponse",
+        name: filename,
         data: { filename: filename }
     },
 
diff --git a/cfg/utils.jsonnet b/cfg/utils.jsonnet
index 4441e63..e715b2c 100644
--- a/cfg/utils.jsonnet
+++ b/cfg/utils.jsonnet
@@ -4,6 +4,17 @@
     // Return true if string s has at least one % symbol.
     haspct(s, pct="%"):: std.length(std.findSubstr(pct, s))>0,
 
+    stripext(fn, n=1) :: {
+        local parts = std.split(fn, "."),
+        local siz = std.length(parts),
+        ret: std.join(".", parts[:siz+1-n])
+    }.ret,
+
+    basename(fn) :: {
+        local parts = std.split(fn, "/"),
+        ret: parts[std.length(parts)-1]
+    }.ret,
+
     // append a suffix to the base name of a file name, prior to .ext
     basename_append(filename, suffix) :: {
         local l = std.split(filename, "."),
diff --git a/testit.sh b/testit.sh
index e4ff9fe..abdda7e 100755
--- a/testit.sh
+++ b/testit.sh
@@ -5,50 +5,53 @@ set -x
 mkdir -p testit
 
 tiers=(orig gauss)
-
-taps=""
-for tier in ${tiers[*]}
+for domain in real fake
 do
-    taps+="{\"$tier\":\"testit/fake-frames-${tier}.npz\"}"
-done
+    taps=""
+    for tier in ${tiers[*]}
+    do
+        taps+="{\"$tier\":\"testit/${domain}-frames-${tier}.npz\"}"
+    done
 
-if [ -f testit/depos.npz ] ; then
-    echo "depos already generated"
-else
-    wirecell-gen depo-lines \
-    --seed 1234 \
-    --tracks 100 \
-    --sets 1 \
-    --diagonal '16000.0*mm,6100.0*mm,7000.0*mm' \
-    --corner   '-8000.0*mm,0.0*mm,0.0*mm' \
-    --output testit/depos.npz || exit
-fi
-
-if [ -f testit/fake-frames-orig-apa0.npz ] ; then
-    echo "wire-cell has run already, rm testit if you want"
-else
-    wire-cell \
-        -l stdout -L debug -P cfg\
-        -A input=testit/depos.npz \
-        --tla-code taps=$taps \
-        -A wires=data/wires/wires.json.bz2  \
-        -A resps=data/resps/fake-resps.json.bz2 \
-        -A thread=multi \
-        -A noisef=protodune-noise-spectra-v1.json.bz2 \
-        -c cfg/main-depos-sigproc.jsonnet || exit 
-fi
-
-
-for tier in orig gauss
-do
-    for apaid in 0 1 2 3 4 5
+    if [ -f testit/depos.npz ] ; then
+        echo "depos already generated"
+    else
+        wirecell-gen depo-lines \
+                     --seed 1234 \
+                     --tracks 100 \
+                     --sets 1 \
+                     --diagonal '16000.0*mm,6100.0*mm,7000.0*mm' \
+                     --corner   '-8000.0*mm,0.0*mm,0.0*mm' \
+                     --output testit/depos.npz || exit
+    fi
+
+    if [ -f testit/${domain}-frames-orig-apa0.npz ] ; then
+        echo "wire-cell has run already for $domain"
+    else
+        wire-cell \
+            -l stdout -L debug -P cfg\
+            -A input=testit/depos.npz \
+            --tla-code taps=$taps \
+            -A wires=data/wires/wires.json.bz2  \
+            -A resps_sim=data/resps/${domain}-resps.json.bz2 \
+            -A resps_sigproc=data/resps/fake-resps.json.bz2 \
+            -A thread=multi \
+            -A noisef=protodune-noise-spectra-v1.json.bz2 \
+            -c cfg/main-depos-sigproc.jsonnet || exit 
+    fi
+
+
+    for tier in orig gauss
     do
-        tag=${tier}${apaid}
-        wirecell-gen \
-            plot-sim \
-            testit/fake-frames-${tier}-apa${apaid}.npz \
-            -p frames -b 0,2560 --tag ${tier}${apaid} \
-            testit/fake-frames-${tier}-apa${apaid}.png || exit
+        for apaid in 0 1 2 3 4 5
+        do
+            tag=${tier}${apaid}
+            wirecell-gen \
+                plot-sim \
+                testit/${domain}-frames-${tier}-apa${apaid}.npz \
+                -p frames -b 0,2560 --tag ${tier}${apaid} \
+                testit/${domain}-frames-${tier}-apa${apaid}.png || exit
+        done
     done
 done
 

From 68cc1bd27b7d49a93ab6cb67a1d96ad06e1bcbfc Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Thu, 29 Jul 2021 15:43:22 -0400
Subject: [PATCH 09/15] Remove mkdir now that WCT handles it and fix thread
 option pass through

---
 Snakefile | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/Snakefile b/Snakefile
index a2e7881..bb49813 100644
--- a/Snakefile
+++ b/Snakefile
@@ -19,14 +19,15 @@ datadir = os.path.abspath(os.path.join(outdir, datadir))
 plotdir = os.path.abspath(os.path.join(outdir, plotdir))
     
 seed = config.get("seed", "1,2,3,4")
-ntracks = config.get("ntracks", 10)
-nevents = config.get("nevents", 10)
+ntracks = int(config.get("ntracks", 10))
+nevents = int(config.get("nevents", 10))
 wcloglvl = config.get("wcloglvl", "info")
 
 # limit number of threads per wire-cell job
-threads = config.get("threads", 1)
+wct_threads = int(config.get("threads", 1))
 # single threaded uses Pgrapher, multi uses TbbFlow
-threading = "single" if threads == 1 else "multi"
+wct_threading = "single" if wct_threads == 1 else "multi"
+print(f'WCT THREADS {wct_threads} ({wct_threading})')
 
 # The rest are hard wired for now
 wcdata_url = "https://github.com/WireCell/wire-cell-data/raw/master"
@@ -233,11 +234,9 @@ rule sim_frames:
         taps = frame_taps
     shell: '''
     rm -f {output}; 
-    mkdir -p {datadir}/frames/orig;
-    mkdir -p {datadir}/frames/gauss;
     wire-cell \
-    --threads 4 \
-    -A thread={threading} \
+    --threads {wct_threads} \
+    -A thread={wct_threading} \
     -l stdout -L {config[wcloglvl]} \
     -P cfg \
     -A input={input.depos} \
@@ -249,6 +248,10 @@ rule sim_frames:
     -c {input.config}
     '''
         
+    ## remove to check WCT makes output directories
+    # mkdir -p {datadir}/frames/orig;
+    # mkdir -p {datadir}/frames/gauss;
+
 def gen_plot_frames(w):
     i = int(w.apa)
     tag = f"{w.tier}{i}"

From c6d5f1b10e14a3a8f5d7f6f3621291aa44bc00dd Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Thu, 29 Jul 2021 18:06:19 -0400
Subject: [PATCH 10/15] Tweak plots

---
 Snakefile | 47 ++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 38 insertions(+), 9 deletions(-)

diff --git a/Snakefile b/Snakefile
index bb49813..514a442 100644
--- a/Snakefile
+++ b/Snakefile
@@ -328,12 +328,38 @@ rule split_images:
     {input}
     '''
 
-def gen_title(w):
+def plot_split_params(w):
     if w.domain == 'real':
         dim='2D'
     else:
         dim='q1D'
-    return f'"{w.tier} {w.domain}/{dim}, event {w.event}, APA {w.apa}, {w.plane} plane"',
+
+    if w.tier == "orig":
+        ztitle='ADC (baseline subtracted)'
+        vmin=-50
+        vmax=50
+        baseline="median"
+    else:
+        ztitle='Signal (ionization electrons)'
+        vmin=0
+        vmax=5000
+        baseline="0"
+
+    blerg="0"
+    if int(w.zoomlevel) == 2:
+        blerg=""
+
+    if w.plane == "U":
+        zoom=f'0:80{blerg},0:400{blerg}'
+    elif w.plane == "V":
+        zoom=f'0:80{blerg},0:400{blerg}'
+    elif w.plane == "W":
+        zoom=f'0:96{blerg},0:400{blerg}'
+
+    title=f'{w.tier} {w.domain}/{dim}, event {w.event}, APA {w.apa}, {w.plane} plane'
+    return locals()
+
+
 
 ## Note, we must match the input here by hand to the output above
 ## because the domain is not included in the expand above but is here.
@@ -342,17 +368,19 @@ rule plot_split_images:
     input:
         datadir+'/images/{tier}/{domain}/protodune-{tier}{apa}-{event}-{plane}.npz',
     output:
-        plotdir+'/images/{tier}/{domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}.{ext}'
+        plotdir+'/images/{tier}/{domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}-zoom{zoomlevel}.{ext}'
     params:
-        title = gen_title
+        p = plot_split_params
     shell: '''
     wirecell-util npz-to-img --cmap {wildcards.cmap} \
-    --title {params.title} \
+    --title '{params.p[title]}' \
     --xtitle 'Relative ticks number' \
     --ytitle 'Relative channel number' \
-    --ztitle 'ADC (baseline subtracted)' \
-    --zoom 300:500,0:1000 --mask 0 --vmin -50 --vmax 50 \
-    --dpi 600 --baseline=median -o {output} {input}
+    --ztitle '{params.p[ztitle]}' \
+    --zoom '{params.p[zoom]}' \
+    --vmin '{params.p[vmin]}' --vmax '{params.p[vmax]}' \
+    --mask 0 \
+    --dpi 600 --baseline='{params.p[baseline]}' -o {output} {input}
     '''
 
 rule just_images:
@@ -371,8 +399,9 @@ rule all_images:
             domain = ["real","fake"],
             tier = TIERS,
             event  = [0], apa=[0], plane=["U","V","W"],
-            ext    = ["png", "pdf", "svg"],
+            ext    = ["png"], # , "pdf", "svg"],
             cmap   = ["seismic", "viridis"],
+            zoomlevel=[1, 2],
         )
 
 

From a516c6586b1a8a07af6259e7253b9dac60ae14cf Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Tue, 3 Aug 2021 17:18:38 -0400
Subject: [PATCH 11/15] Add depo splat job as well as 2x2 outer product of
 (fake,real)x(sim,sigproc)

---
 Snakefile                      | 183 ++++++++++++++++++++++++---------
 cfg/main-depos-sigproc.jsonnet |   3 +-
 cfg/main-depos-splat.jsonnet   |  76 ++++++++++++++
 cfg/toyzero.jsonnet            |  22 ++++
 4 files changed, 231 insertions(+), 53 deletions(-)
 create mode 100644 cfg/main-depos-splat.jsonnet

diff --git a/Snakefile b/Snakefile
index 514a442..0a4aabc 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,7 +1,7 @@
 #!/usr/bin/env snakemake
 
-import json
 import os
+import json
 from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
 HTTP = HTTPRemoteProvider()
 
@@ -51,7 +51,8 @@ DOMAINS = ["fake", "real"]
 # The data tiers for frame or image. We make all tiers in one job.
 # The 'orig' is the output of the simulation and 'gauss' is the output
 # of signal processing using the charge-preserving filters.
-TIERS = ["orig", "gauss"]
+SIM_TIERS = ["orig", "gauss"]
+TIERS = SIM_TIERS + ["splat"]
 
 # some important file names
 real_resps    = f'{datadir}/resps/real-resps.{wcdata_ext}'
@@ -169,13 +170,15 @@ rule all_depos:
 
 # frames
 
-wct_cfg_file = 'cfg/main-depos-sigproc.jsonnet'
+
+wct_sigproc_cfg = 'cfg/main-depos-sigproc.jsonnet'
+wct_splat_cfg = 'cfg/main-depos-splat.jsonnet'
 
 # note, we pass bogus TLAs so don't use the generated json for
 # anything real!
 rule wct_dots:
     input:
-        config = wct_cfg_file
+        config = wct_sigproc_cfg
     output:
         json = temp(f'{plotdir}/dots/cfg.json'),
         dot  = temp(f'{plotdir}/dots/dag.dot'),
@@ -203,10 +206,10 @@ rule all_dots:
 # this gives the pattern for one per-APA frame file.  The %d is
 # interpolated by wire-cell configuration.
 
-frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.npz'
+frames_wildcard = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa{{apa}}.npz'
 
 def frame_taps(w):
-    frames_pattern = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa%d.npz'
+    frames_pattern = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa%d.npz'
     taps = list()
     for tier in ('orig', 'gauss'):
         d = dict(w)
@@ -216,20 +219,20 @@ def frame_taps(w):
     taps = ",".join(taps)
     return '{%s}'%taps
 
-def frame_files():
-    frames_pattern = datadir + '/frames/{tier}/{{domain}}-frames-apa{apaid}.npz'
-    return expand(frames_pattern, tier=TIERS, apaid = apa_iota)
+def sim_frame_files():
+    frames_pattern = datadir + '/frames/{tier}/{{sim_domain}}-{{sigproc_domain}}-frames-apa{apaid}.npz'
+    return expand(frames_pattern, tier=SIM_TIERS, apaid = apa_iota)
 
 rule sim_frames:
     input:
         wires = wires_file,
-        resps_sim = domain_resps,
-        resps_sigproc = fake_resps,
+        resps_sim = f'{datadir}/resps/{{sim_domain}}-resps.{wcdata_ext}',
+        resps_sigproc = f'{datadir}/resps/{{sigproc_domain}}-resps.{wcdata_ext}',
         depos = depos_file,
-        config = wct_cfg_file,
+        config = wct_sigproc_cfg,
         noise = noise_file
     output:
-        temp(frame_files())
+        temp(sim_frame_files())
     params:
         taps = frame_taps
     shell: '''
@@ -248,9 +251,30 @@ rule sim_frames:
     -c {input.config}
     '''
         
-    ## remove to check WCT makes output directories
-    # mkdir -p {datadir}/frames/orig;
-    # mkdir -p {datadir}/frames/gauss;
+
+# like sim_frames but we use DepoSplat instead of sim+sigproc.
+rule splat_frames:
+    input:
+        wires = wires_file,
+        depos = depos_file,
+        config = wct_splat_cfg
+    output:
+        temp([f'{datadir}/frames/splat/splat-frames-apa{apa}.npz' for apa in apa_iota])
+    params:
+        taps = f'{{"splat":"{datadir}/frames/splat/splat-frames-apa%d.npz"}}'
+    shell: '''
+    rm -f {output}; 
+    wire-cell \
+    --threads {wct_threads} \
+    -A thread={wct_threading} \
+    -l stdout -L {config[wcloglvl]} \
+    -P cfg \
+    -A input={input.depos} \
+    --tla-code 'taps={params.taps}' \
+    -A wires={input.wires} \
+    -c  {input.config}
+    '''
+
 
 def gen_plot_frames(w):
     i = int(w.apa)
@@ -261,28 +285,50 @@ rule plot_frames:
     input:
         frames_wildcard
     output:
-        f'{plotdir}/frames-{{tier}}-{{domain}}-apa{{apa}}.{{ext}}'
+        f'{plotdir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-apa{{apa}}.{{ext}}'
     params:
         p = gen_plot_frames
     shell:'''
     wirecell-gen plot-sim {input} {output} -p frames -b {params.p[chb]} --tag "{params.p[tag]}"
     '''
 
+rule plot_splat_frames:
+    input:
+        f'{datadir}/frames/splat/splat-frames-apa{{apa}}.npz'
+    output:
+        f'{plotdir}/frames/splat/splat-apa{{apa}}.{{ext}}'
+    shell:'''
+    wirecell-gen plot-sim {input} {output} -p frames -b 0,2560 --tag splat{wildcards.apa}"
+    '''
+
 rule plot_frames_hidpi:
     input:
-        f'{plotdir}/frames-{{tier}}-{{domain}}-apa{{apa}}.pdf'
+        f'{plotdir}/frames-{{tier}}-{{sim_domain}}-{{sigproc_domain}}-apa{{apa}}.pdf'
     output:
-        f'{plotdir}/hidpi/frames-{{tier}}-{{domain}}-apa{{apa}}.png'
-    params:
+        f'{plotdir}/hidpi/frames-{{tier}}-{{sim_domain}}-{{sigproc_domain}}-apa{{apa}}.png'
 
     shell:'''
     pdftoppm -rx 600 -ry 600 {input} | pnmtopng > {output}
     '''
 
 
+rule just_splat_frames:
+    input:
+        rules.splat_frames.output
+
+rule all_splat_frames:
+    input:
+        rules.just_splat_frames.input,        
+        expand(rules.plot_splat_frames.output,
+               ext=["png","pdf"], apa=apa_iota)
+    
+
 rule just_frames:
     input:
-        expand(rules.sim_frames.output, domain=["real","fake"]),
+        expand(rules.sim_frames.output,
+               sim_domain=["real","fake"],
+               sigproc_domain=["real","fake"],
+               ),
         
 
 rule all_frames:
@@ -291,11 +337,16 @@ rule all_frames:
         rules.all_wires.input,
         rules.all_depos.input,
         rules.just_frames.input,
-        expand(rules.plot_frames.output, domain=["real","fake"],
-               tier=TIERS,
+        expand(rules.plot_frames.output,
+               sim_domain=["real","fake"],
+               sigproc_domain=["real","fake"],
+               tier=SIM_TIERS,
                ext=["png","pdf"], apa=apa_iota),
-        expand(rules.plot_frames_hidpi.output, domain=["real","fake"],
-               tier=TIERS, apa=[0])
+
+        # expand(rules.plot_frames_hidpi.output,
+        #        sim_domain=["real","fake"],
+        #        sigproc_domain=["real","fake"],
+        #        tier=TIERS, apa=[0])
 
 
 
@@ -316,23 +367,49 @@ split_outer_product = dict(
 
 # frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.npz'
 
+# this pattern is formatted inside wirecell-util frame-split.
+split_array_pattern = '{detector}-{tag}-{index}-{planeletter}'
+
+sigproc_rebin = 4
+def rebin_number(w):
+    if w.tier == "orig":
+        return 0;
+    return sigproc_rebin
+
 rule split_images:
     input:
         frames_wildcard
     output:
-        expand(datadir+'/images/{{tier}}/{{domain}}/protodune-{{tier}}{{apa}}-{event}-{plane}.npz',
+        expand(datadir+'/images/{{tier}}/{{sim_domain}}-{{sigproc_domain}}/protodune-{{tier}}{{apa}}-{event}-{plane}.npz',
                **split_outer_product)
-    shell: '''
-    wirecell-util frame-split \
-    -f {datadir}/images/{wildcards.tier}/{wildcards.domain}/{{detector}}-{{tag}}-{{index}}-{{planeletter}}.npz \
-    {input}
-    '''
+    params:
+        outpath = datadir+'/images/{tier}/{sim_domain}-{sigproc_domain}',
+        mdpath = 'metadata-{apa}.json',
+        rebin = rebin_number
+    run:
+        if not os.path.exists(params.outpath):
+            os.makedirs(params.outpath)
+        mdpath = os.path.join(params.outpath, params.mdpath)
+        with open(mdpath, "w") as fp:
+            fp.write(json.dumps(dict(wildcards), indent=4))
+        shell('wirecell-util frame-split -r {params.rebin} -m {mdpath} -a {params.outpath}/{split_array_pattern} {input}')
+
 
 def plot_split_params(w):
-    if w.domain == 'real':
-        dim='2D'
+    if w.tier == 'splat':
+        dim="splat"
+    elif w.sim_domain == 'real':
+        dim='sim:2D'
     else:
-        dim='q1D'
+        dim='sim:q1D'
+
+    if w.tier == "gauss":
+        # only one response is relevant to ADC tier
+        # signals may have a different response used in decon.
+        if w.sigproc_domain == 'real':
+            dim+='/SP:2D'
+        else:
+            dim+='/SP:q1D'
 
     if w.tier == "orig":
         ztitle='ADC (baseline subtracted)'
@@ -342,21 +419,23 @@ def plot_split_params(w):
     else:
         ztitle='Signal (ionization electrons)'
         vmin=0
-        vmax=5000
+        vmax=20000
         baseline="0"
 
-    blerg="0"
-    if int(w.zoomlevel) == 2:
-        blerg=""
-
-    if w.plane == "U":
-        zoom=f'0:80{blerg},0:400{blerg}'
-    elif w.plane == "V":
-        zoom=f'0:80{blerg},0:400{blerg}'
-    elif w.plane == "W":
-        zoom=f'0:96{blerg},0:400{blerg}'
+    # we make 2 zoom levels.  1 is full, 2 is something less.
+    factor = 2
+    if int(w.zoomlevel) == 1:
+        factor = 10
+    if w.plane == "W":
+        chanmax=96*factor
+    else:
+        chanmax=80*factor
+    tickmax=400*factor
+    if w.tier != "orig":
+        tickmax = tickmax // sigproc_rebin
+    zoom=f'0:{chanmax},0:{tickmax}'
 
-    title=f'{w.tier} {w.domain}/{dim}, event {w.event}, APA {w.apa}, {w.plane} plane'
+    title=f'{w.tier} {dim}, event {w.event}, APA {w.apa}, {w.plane} plane'
     return locals()
 
 
@@ -366,9 +445,9 @@ def plot_split_params(w):
 ## Above is 1->N, here is 1->1.
 rule plot_split_images:
     input:
-        datadir+'/images/{tier}/{domain}/protodune-{tier}{apa}-{event}-{plane}.npz',
+        datadir+'/images/{tier}/{sim_domain}-{sigproc_domain}/protodune-{tier}{apa}-{event}-{plane}.npz',
     output:
-        plotdir+'/images/{tier}/{domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}-zoom{zoomlevel}.{ext}'
+        plotdir+'/images/{tier}/{sim_domain}-{sigproc_domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}-zoom{zoomlevel}.{ext}'
     params:
         p = plot_split_params
     shell: '''
@@ -387,7 +466,8 @@ rule just_images:
     input:
         rules.just_frames.input,
         expand(rules.split_images.output,
-               domain=["real","fake"],
+               sim_domain=["real","fake"],
+               sigproc_domain=["real","fake"],
                tier=["gauss"], apa=apa_iota)
 
 ## note, list-of-list for the split_images rule
@@ -396,8 +476,9 @@ rule all_images:
         rules.just_images.input,
         expand(
             rules.plot_split_images.output,
-            domain = ["real","fake"],
-            tier = TIERS,
+            sim_domain = ["real","fake"],
+            sigproc_domain = ["real","fake"],
+            tier = SIM_TIERS,
             event  = [0], apa=[0], plane=["U","V","W"],
             ext    = ["png"], # , "pdf", "svg"],
             cmap   = ["seismic", "viridis"],
diff --git a/cfg/main-depos-sigproc.jsonnet b/cfg/main-depos-sigproc.jsonnet
index 78b9262..2fc5cc3 100644
--- a/cfg/main-depos-sigproc.jsonnet
+++ b/cfg/main-depos-sigproc.jsonnet
@@ -14,12 +14,11 @@
 //    -A depos=depos.npz \
 //    -A taps={...see below...} \
 //    -A wires=wires-geometry.json.bz2 \
-//    -A resps=field-response.json.bz2 \
 //    -A resps_sim=field-response-for-sim.json.bz2 \
 //    -A resps_sigproc=field-response-for-sigproc.json.bz2 \
 //    -A noisef=/path/to/noise/model/file \
 //    -A thread=[single|multi] \
-//    -c main-depos-sim-adc.jsonnet
+//    -c main-depos-sigproc.jsonnet
 //
 // The 'noisef' TLA is optional and specifies a noise model file.  If
 // not given, only signal is simulated.
diff --git a/cfg/main-depos-splat.jsonnet b/cfg/main-depos-splat.jsonnet
new file mode 100644
index 0000000..fb888ff
--- /dev/null
+++ b/cfg/main-depos-splat.jsonnet
@@ -0,0 +1,76 @@
+// This is a main wire-cell configuration file.
+//
+// It implements the chain:
+//   (depos)->splat->(signals)
+//
+// It takes a number of top-level-arguments (TLA) which can control
+// input configuration and input data and a number of output data
+// "taps".  You may also control if it runs in single or multi thread
+// mode
+//
+// Run like
+//
+//  wire-cell \
+//    -A depos=depos.npz \
+//    -A taps={...see below...} \
+//    -A wires=wires-geometry.json.bz2 \
+//    -A thread=[single|multi] \
+//    -c main-depos-splat.jsonnet
+//
+// If "taps" is given it specifies a mapping from a data tier key word
+// to a file name.  The key is one of the conventional tags:
+//
+// - splat :: the output of DepoSplat.
+//
+// The file name may have a "%" formatter which will be interpolated
+// against the APA ID number.  If omitted, "-apa%d" will be inserted
+// at the end of the base file name just prior to the extention
+// (likely .npz).
+
+local wc = import "wirecell.jsonnet";
+local pg = import "pgraph.jsonnet";
+
+local tz = import "toyzero.jsonnet";
+local io = import "ioutils.jsonnet";
+
+local params = import "pgrapher/experiment/pdsp/simparams.jsonnet";
+local spfilt = import "pgrapher/experiment/pdsp/sp-filters.jsonnet";
+local chndb = import "pdsp_chndb.jsonnet";
+
+function(input, taps, wires, thread='single')
+    local app = if thread == 'single'
+                then 'Pgrapher'
+                else 'TbbFlow';
+    local seeds = [0,1,2,3,4];  // maybe let CLI set?
+    local depos = io.npz_source_depo("depos", input);
+
+
+    local wireobj = tz.wire_file(wires);
+    local anodes = tz.anodes(wireobj, params.det.volumes);
+
+    local apaids = std.range(0, std.length(anodes)-1);
+
+    local random = tz.random(seeds);
+
+    local drifter = tz.drifter(params.det.volumes, params.lar, random);
+
+    local tap_out(tap, apaid) =
+        if std.objectHas(taps, tap)
+        then [io.frame_out(tap+"%d", apaid, taps[tap], tags=[tap+"%d"], cap = tap=="gauss")]
+        else [];
+
+    local splat(n, ) = [
+        local anode = anodes[n];
+        tz.splat(anode, params.daq, params.lar)
+    ] + tap_out("splat", n);
+
+    local oneapa(n) = pg.pipeline(splat(n));
+
+    local pipes = [oneapa(n) for n in apaids];
+
+    local body = pg.fan.fanout('DepoFanout', pipes);
+    local full = pg.pipeline([depos, drifter, body]);
+
+    tz.main(full, app)
+
+
diff --git a/cfg/toyzero.jsonnet b/cfg/toyzero.jsonnet
index 35b2c88..62c76f2 100644
--- a/cfg/toyzero.jsonnet
+++ b/cfg/toyzero.jsonnet
@@ -218,6 +218,28 @@ local ut = import "utils.jsonnet";
         pipeline: pg.pipeline(beg + mid + end),
     }.pipeline,
 
+
+    // Return a DepoSplat node
+    splat(anode, daq, lar) :: pg.pnode({
+        type: "DepoSplat",
+        name: "splat%d"%anode.data.ident,
+        data: {
+            tag: "splat",
+            anode: wc.tn(anode),
+            continuous: false,
+            fixed: true,
+            drift_speed: lar.drift_speed,
+            readout_time: daq.nticks*daq.tick, 
+            start_time: 0,
+            tick: daq.tick,
+            nsigma: 3,
+        }
+    }, nin=1, nout=1, uses=[anode]),
+
+
+
+    // top-level stuff
+
     local plugins = [
         "WireCellSio", "WireCellAux",
         "WireCellGen", "WireCellSigProc",

From 01547d18f3815f3c805c429a4dce082c1be5cb12 Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Thu, 5 Aug 2021 14:48:32 -0400
Subject: [PATCH 12/15] Fix depo times, add 'splat' sim+sigproc

---
 Snakefile                    | 147 +++++++++++++++++++++++++----------
 cfg/main-depos-splat.jsonnet |   2 +-
 cfg/toyzero.jsonnet          |  60 ++++++++++----
 3 files changed, 153 insertions(+), 56 deletions(-)

diff --git a/Snakefile b/Snakefile
index 0a4aabc..b1bd10a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -21,6 +21,7 @@ plotdir = os.path.abspath(os.path.join(outdir, plotdir))
 seed = config.get("seed", "1,2,3,4")
 ntracks = int(config.get("ntracks", 10))
 nevents = int(config.get("nevents", 10))
+depotimes = config.get("depotimes", "-3*ms,6*ms")
 wcloglvl = config.get("wcloglvl", "info")
 
 # limit number of threads per wire-cell job
@@ -147,6 +148,7 @@ rule gen_depos:
         temp(depos_file)
     shell: '''
     wirecell-gen depo-lines \
+    --time {depotimes} \
     --seed {seed} \
     --tracks {ntracks} --sets {nevents} \
     --diagonal '{params.diag}' --corner '{params.corn}' \
@@ -298,17 +300,7 @@ rule plot_splat_frames:
     output:
         f'{plotdir}/frames/splat/splat-apa{{apa}}.{{ext}}'
     shell:'''
-    wirecell-gen plot-sim {input} {output} -p frames -b 0,2560 --tag splat{wildcards.apa}"
-    '''
-
-rule plot_frames_hidpi:
-    input:
-        f'{plotdir}/frames-{{tier}}-{{sim_domain}}-{{sigproc_domain}}-apa{{apa}}.pdf'
-    output:
-        f'{plotdir}/hidpi/frames-{{tier}}-{{sim_domain}}-{{sigproc_domain}}-apa{{apa}}.png'
-
-    shell:'''
-    pdftoppm -rx 600 -ry 600 {input} | pnmtopng > {output}
+    wirecell-gen plot-sim {input} {output} -p frames -b 0,2560 --tag splat{wildcards.apa}
     '''
 
 
@@ -320,7 +312,7 @@ rule all_splat_frames:
     input:
         rules.just_splat_frames.input,        
         expand(rules.plot_splat_frames.output,
-               ext=["png","pdf"], apa=apa_iota)
+               ext=["png"], apa=apa_iota)
     
 
 rule just_frames:
@@ -341,7 +333,7 @@ rule all_frames:
                sim_domain=["real","fake"],
                sigproc_domain=["real","fake"],
                tier=SIM_TIERS,
-               ext=["png","pdf"], apa=apa_iota),
+               ext=["png"], apa=apa_iota),
 
         # expand(rules.plot_frames_hidpi.output,
         #        sim_domain=["real","fake"],
@@ -375,6 +367,12 @@ def rebin_number(w):
     if w.tier == "orig":
         return 0;
     return sigproc_rebin
+def tick_offset(w):
+    if w.tier == 'splat':
+        # approx, chosen by comparing gauss W to splat W plots
+        # this is pre-rebin ticks, 0.5us.
+        return 125+8
+    return 0
 
 rule split_images:
     input:
@@ -385,14 +383,34 @@ rule split_images:
     params:
         outpath = datadir+'/images/{tier}/{sim_domain}-{sigproc_domain}',
         mdpath = 'metadata-{apa}.json',
-        rebin = rebin_number
+        rebin = rebin_number,
+        tickoff = tick_offset
+    run:
+        if not os.path.exists(params.outpath):
+            os.makedirs(params.outpath)
+        mdpath = os.path.join(params.outpath, params.mdpath)
+        with open(mdpath, "w") as fp:
+            fp.write(json.dumps(dict(wildcards), indent=4))
+        shell('wirecell-util frame-split -t {params.tickoff} -r {params.rebin} -m {mdpath} -a {params.outpath}/{split_array_pattern} {input}')
+
+rule split_splat_images:
+    input:
+        f'{datadir}/frames/splat/splat-frames-apa{{apa}}.npz'
+    output:
+        expand(datadir+'/images/{{tier}}/splat/protodune-{{tier}}{{apa}}-{event}-{plane}.npz',
+               **split_outer_product)
+    params:
+        outpath = datadir+'/images/{tier}/splat',
+        mdpath = 'metadata-{apa}.json',
+        rebin = rebin_number,
+        tickoff = tick_offset
     run:
         if not os.path.exists(params.outpath):
             os.makedirs(params.outpath)
         mdpath = os.path.join(params.outpath, params.mdpath)
         with open(mdpath, "w") as fp:
             fp.write(json.dumps(dict(wildcards), indent=4))
-        shell('wirecell-util frame-split -r {params.rebin} -m {mdpath} -a {params.outpath}/{split_array_pattern} {input}')
+        shell('wirecell-util frame-split -t {params.tickoff} -r {params.rebin} -m {mdpath} -a {params.outpath}/{split_array_pattern} {input}')
 
 
 def plot_split_params(w):
@@ -422,20 +440,26 @@ def plot_split_params(w):
         vmax=20000
         baseline="0"
 
-    # we make 2 zoom levels.  1 is full, 2 is something less.
-    factor = 2
-    if int(w.zoomlevel) == 1:
-        factor = 10
-    if w.plane == "W":
-        chanmax=96*factor
-    else:
-        chanmax=80*factor
-    tickmax=400*factor
+    # we make 2 zoom levels.  1 is full, 2 is something zoomed in.
+
+    chan0 = 0
+    nchans = 960 if w.plane == "W" else 800
+    tick0 = 0
+    nticks = 6000
+
+    # pick a region with good activity in all 3 views
+    if int(w.zoomlevel) == 2:
+        nchans = int(nchans / 5)
+        tick0 = 3600
+        nticks = 800
+
     if w.tier != "orig":
-        tickmax = tickmax // sigproc_rebin
-    zoom=f'0:{chanmax},0:{tickmax}'
+        tick0 = int(tick0/sigproc_rebin)
+        nticks = int(nticks/sigproc_rebin)
+
+    zoom = f'{chan0}:{chan0+nchans},{tick0}:{tick0+nticks}'
+    title = f'{w.tier} {dim}, event {w.event}, APA {w.apa}, {w.plane} plane'
 
-    title=f'{w.tier} {dim}, event {w.event}, APA {w.apa}, {w.plane} plane'
     return locals()
 
 
@@ -443,14 +467,7 @@ def plot_split_params(w):
 ## Note, we must match the input here by hand to the output above
 ## because the domain is not included in the expand above but is here.
 ## Above is 1->N, here is 1->1.
-rule plot_split_images:
-    input:
-        datadir+'/images/{tier}/{sim_domain}-{sigproc_domain}/protodune-{tier}{apa}-{event}-{plane}.npz',
-    output:
-        plotdir+'/images/{tier}/{sim_domain}-{sigproc_domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}-zoom{zoomlevel}.{ext}'
-    params:
-        p = plot_split_params
-    shell: '''
+plot_split_shell = '''
     wirecell-util npz-to-img --cmap {wildcards.cmap} \
     --title '{params.p[title]}' \
     --xtitle 'Relative ticks number' \
@@ -461,6 +478,23 @@ rule plot_split_images:
     --mask 0 \
     --dpi 600 --baseline='{params.p[baseline]}' -o {output} {input}
     '''
+rule plot_split_images:
+    input:
+        datadir+'/images/{tier}/{sim_domain}-{sigproc_domain}/protodune-{tier}{apa}-{event}-{plane}.npz',
+    output:
+        plotdir+'/images/{tier}/{sim_domain}-{sigproc_domain}/{cmap}/protodune-{tier}{apa}-{event}-{plane}-zoom{zoomlevel}.{ext}'
+    params:
+        p = plot_split_params
+    shell: plot_split_shell
+
+rule plot_split_splat_images:
+    input:
+        datadir+'/images/{tier}/splat/protodune-{tier}{apa}-{event}-{plane}.npz',
+    output:
+        plotdir+'/images/{tier}/splat/{cmap}/protodune-{tier}{apa}-{event}-{plane}-zoom{zoomlevel}.{ext}'
+    params:
+        p = plot_split_params
+    shell: plot_split_shell
 
 rule just_images:
     input:
@@ -470,18 +504,53 @@ rule just_images:
                sigproc_domain=["real","fake"],
                tier=["gauss"], apa=apa_iota)
 
+rule just_splat_images:
+    input:
+        rules.just_splat_frames.input,
+        expand(rules.split_splat_images.output,
+               tier=["splat"], apa=apa_iota)
+
 ## note, list-of-list for the split_images rule
 rule all_images:
     input:
         rules.just_images.input,
+        rules.just_splat_images.input,
+        expand(
+            rules.plot_split_images.output,
+            sim_domain = ["fake"],
+            sigproc_domain = ["fake"],
+            tier = ["orig"],
+            event  = [0], apa=apa_iota, plane=["U","V","W"],
+            ext    = ["png"],
+            cmap   = ["seismic"],
+            zoomlevel=[1, 2],
+        ),
+        expand(
+            rules.plot_split_images.output,
+            sim_domain = ["real"],
+            sigproc_domain = ["real"],
+            tier = ["orig"],
+            event  = [0], apa=apa_iota, plane=["U","V","W"],
+            ext    = ["png"],
+            cmap   = ["seismic"],
+            zoomlevel=[1, 2],
+        ),
         expand(
             rules.plot_split_images.output,
             sim_domain = ["real","fake"],
             sigproc_domain = ["real","fake"],
-            tier = SIM_TIERS,
-            event  = [0], apa=[0], plane=["U","V","W"],
-            ext    = ["png"], # , "pdf", "svg"],
-            cmap   = ["seismic", "viridis"],
+            tier = ["gauss"],
+            event  = [0], apa=apa_iota, plane=["U","V","W"],
+            ext    = ["png"],
+            cmap   = ["viridis"],
+            zoomlevel=[1, 2],
+        ),
+        expand(
+            rules.plot_split_splat_images.output,
+            tier = ["splat"],
+            event  = [0], apa=apa_iota, plane=["U","V","W"],
+            ext    = ["png"],
+            cmap   = ["viridis"],
             zoomlevel=[1, 2],
         )
 
diff --git a/cfg/main-depos-splat.jsonnet b/cfg/main-depos-splat.jsonnet
index fb888ff..5aca79f 100644
--- a/cfg/main-depos-splat.jsonnet
+++ b/cfg/main-depos-splat.jsonnet
@@ -61,7 +61,7 @@ function(input, taps, wires, thread='single')
 
     local splat(n, ) = [
         local anode = anodes[n];
-        tz.splat(anode, params.daq, params.lar)
+        tz.splat(anode, params.daq, params.lar, random)
     ] + tap_out("splat", n);
 
     local oneapa(n) = pg.pipeline(splat(n));
diff --git a/cfg/toyzero.jsonnet b/cfg/toyzero.jsonnet
index 62c76f2..4fda8a0 100644
--- a/cfg/toyzero.jsonnet
+++ b/cfg/toyzero.jsonnet
@@ -188,7 +188,7 @@ local ut = import "utils.jsonnet";
                 toffset: 0,
                 nticks: daq.nticks,
             },
-        }, nin=1, nout=1),
+        }, nin=1, nout=1, uses=[anode]),
 
         ret: pg.pipeline([ductor, reframer]),
     }.ret,
@@ -220,22 +220,50 @@ local ut = import "utils.jsonnet";
 
 
     // Return a DepoSplat node
-    splat(anode, daq, lar) :: pg.pnode({
-        type: "DepoSplat",
-        name: "splat%d"%anode.data.ident,
-        data: {
-            tag: "splat",
-            anode: wc.tn(anode),
-            continuous: false,
-            fixed: true,
-            drift_speed: lar.drift_speed,
-            readout_time: daq.nticks*daq.tick, 
-            start_time: 0,
-            tick: daq.tick,
-            nsigma: 3,
-        }
-    }, nin=1, nout=1, uses=[anode]),
+    splat(anode, daq, lar, rnd=null) :: {
+
+        local apaid = anode.data.ident,
+        local frame_tag = "splat%d" % apaid,
+
+        local rextra = if std.type(rnd) == "null"
+                       then { data:{}, uses:[] }
+                       else {
+                           data: { fluctuate:true, rng: wc.tn(rnd) },
+                           uses: [rnd]
+                       },
+
+        local splat = pg.pnode({
+            type: "DepoSplat",
+            name: "splat%d"%apaid,
+            data: {
+                frame_tag: frame_tag,
+                anode: wc.tn(anode),
+                continuous: false,
+                fixed: true,
+                drift_speed: lar.drift_speed,
+                readout_time: daq.nticks*daq.tick, 
+                start_time: 0,
+                tick: daq.tick,
+                nsigma: 3,
+            } + rextra.data
+        }, nin=1, nout=1, uses=[anode]+rextra.uses),
+
+        local reframer = pg.pnode({
+            type: 'Reframer',
+            name: 'Reframer%d' % apaid,
+            data: {
+                anode: wc.tn(anode),
+                tags: [],
+                frame_tag: frame_tag,
+                fill: 0.0,
+                tbin: 0,
+                toffset: 0,
+                nticks: daq.nticks,
+            },
+        }, nin=1, nout=1, uses=[anode]),
 
+        ret: pg.pipeline([splat, reframer]),
+    }.ret,
 
 
     // top-level stuff

From 56a03470c452a9576713cc3daa56bf18bd3f8903 Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Tue, 17 Aug 2021 13:09:39 -0400
Subject: [PATCH 13/15] Get working with WCT new support for compressed tar
 streams

---
 Snakefile                      | 51 ++++++++++++++++++++--------------
 cfg/ioutils.jsonnet            | 28 +++++++++++++++++--
 cfg/main-depos-sigproc.jsonnet | 22 ++++++++-------
 cfg/main-depos-splat.jsonnet   | 20 +++++++------
 4 files changed, 79 insertions(+), 42 deletions(-)

diff --git a/Snakefile b/Snakefile
index b1bd10a..9d86c6a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -13,10 +13,12 @@ configfile: "toyzero.yaml"
 ##  $ snakemake --config ntracks=100 [...]
 datadir = config.get("datadir", "data")
 plotdir = config.get("plotdir", "plots")
+logdir = config.get("logdir", "logs")
 outdir = config.get("outdir", os.environ.get("TOYZERO_OUTDIR", "."))
 
 datadir = os.path.abspath(os.path.join(outdir, datadir))
 plotdir = os.path.abspath(os.path.join(outdir, plotdir))
+logdir  = os.path.abspath(os.path.join(outdir, logdir))
     
 seed = config.get("seed", "1,2,3,4")
 ntracks = int(config.get("ntracks", 10))
@@ -176,42 +178,49 @@ rule all_depos:
 wct_sigproc_cfg = 'cfg/main-depos-sigproc.jsonnet'
 wct_splat_cfg = 'cfg/main-depos-splat.jsonnet'
 
+def wct_dots_params(w):
+    if w.verb == "brief":
+        return "--no-params"
+    return ""
 # note, we pass bogus TLAs so don't use the generated json for
 # anything real!
 rule wct_dots:
     input:
         config = wct_sigproc_cfg
     output:
-        json = temp(f'{plotdir}/dots/cfg.json'),
-        dot  = temp(f'{plotdir}/dots/dag.dot'),
-        png  = f'{plotdir}/dots/dag.png',
-        pdf  = f'{plotdir}/dots/dag.pdf'
+        json = temp(f'{plotdir}/dots/cfg-{{verb}}.json'),
+        dot  = temp(f'{plotdir}/dots/dag-{{verb}}.dot'),
+        png  = f'{plotdir}/dots/dag-{{verb}}.png',
+        pdf  = f'{plotdir}/dots/dag-{{verb}}.pdf'
+    params:
+        wct_dots_params
     shell: '''
     mkdir -p {plotdir}/dots;
     wcsonnet \
     -P cfg \
     -A input=DEPOS-FILE \
-    --tla-code taps='{{"orig":"frame-orig.npz","gauss":"frame-gauss.npz"}}' \
+    --tla-code taps='{{"orig":"frame-orig-apa%d.tar.bz2","gauss":"frame-gauss-apa%d.tar.bz2"}}' \
     -A wires=WIRES-FILE \
     -A resps_sim=RESPS-SIM-FILE \
     -A resps_sigproc=RESPS-SIGPROC-FILE \
     -A noisef=NOISE-FILE \
     {input.config} > {output.json};
-    wirecell-pgraph dotify --no-params --jpath=-1 {output.json} {output.dot} ;
+    wirecell-pgraph dotify {params} --jpath=-1 {output.json} {output.dot} ;
     dot -Tpng -o {output.png} {output.dot} ;
     dot -Tpdf -o {output.pdf} {output.dot}
     '''
 rule all_dots:
     input:
-        rules.wct_dots.output
+        expand(rules.wct_dots.output, verb=["full", "brief"])
 
 # this gives the pattern for one per-APA frame file.  The %d is
 # interpolated by wire-cell configuration.
 
-frames_wildcard = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa{{apa}}.npz'
+frames_ext = "tar.bz2"
+frames_wildcard = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa{{apa}}.{frames_ext}'
 
 def frame_taps(w):
-    frames_pattern = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa%d.npz'
+    frames_pattern = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa%d.{frames_ext}'
     taps = list()
     for tier in ('orig', 'gauss'):
         d = dict(w)
@@ -222,7 +231,7 @@ def frame_taps(w):
     return '{%s}'%taps
 
 def sim_frame_files():
-    frames_pattern = datadir + '/frames/{tier}/{{sim_domain}}-{{sigproc_domain}}-frames-apa{apaid}.npz'
+    frames_pattern = datadir + '/frames/{tier}/{{sim_domain}}-{{sigproc_domain}}-frames-apa{apaid}.' + frames_ext
     return expand(frames_pattern, tier=SIM_TIERS, apaid = apa_iota)
 
 rule sim_frames:
@@ -237,6 +246,8 @@ rule sim_frames:
         temp(sim_frame_files())
     params:
         taps = frame_taps
+    benchmark:
+        f'{logdir}/sim-frames-{{sim_domain}}-{{sigproc_domain}}.tsv'
     shell: '''
     rm -f {output}; 
     wire-cell \
@@ -261,9 +272,9 @@ rule splat_frames:
         depos = depos_file,
         config = wct_splat_cfg
     output:
-        temp([f'{datadir}/frames/splat/splat-frames-apa{apa}.npz' for apa in apa_iota])
+        temp([f'{datadir}/frames/splat/splat-frames-apa{apa}.{frames_ext}' for apa in apa_iota])
     params:
-        taps = f'{{"splat":"{datadir}/frames/splat/splat-frames-apa%d.npz"}}'
+        taps = f'{{"splat":"{datadir}/frames/splat/splat-frames-apa%d.{frames_ext}"}}'
     shell: '''
     rm -f {output}; 
     wire-cell \
@@ -296,7 +307,7 @@ rule plot_frames:
 
 rule plot_splat_frames:
     input:
-        f'{datadir}/frames/splat/splat-frames-apa{{apa}}.npz'
+        f'{datadir}/frames/splat/splat-frames-apa{{apa}}.tar.gz'
     output:
         f'{plotdir}/frames/splat/splat-apa{{apa}}.{{ext}}'
     shell:'''
@@ -357,7 +368,7 @@ split_outer_product = dict(
     plane  = ["U","V","W"],
 )
 
-# frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.npz'
+# frames_wildcard = f'{datadir}/frames/{{tier}}/{{domain}}-frames-apa{{apa}}.{frames_ext}'
 
 # this pattern is formatted inside wirecell-util frame-split.
 split_array_pattern = '{detector}-{tag}-{index}-{planeletter}'
@@ -385,6 +396,8 @@ rule split_images:
         mdpath = 'metadata-{apa}.json',
         rebin = rebin_number,
         tickoff = tick_offset
+    benchmark:
+        f'{logdir}/split-images-{{tier}}-{{sim_domain}}-{{sigproc_domain}}-apa{{apa}}.tsv'
     run:
         if not os.path.exists(params.outpath):
             os.makedirs(params.outpath)
@@ -395,7 +408,7 @@ rule split_images:
 
 rule split_splat_images:
     input:
-        f'{datadir}/frames/splat/splat-frames-apa{{apa}}.npz'
+        f'{datadir}/frames/splat/splat-frames-apa{{apa}}.{frames_ext}'
     output:
         expand(datadir+'/images/{{tier}}/splat/protodune-{{tier}}{{apa}}-{event}-{plane}.npz',
                **split_outer_product)
@@ -499,14 +512,11 @@ rule plot_split_splat_images:
 rule just_images:
     input:
         rules.just_frames.input,
+        rules.just_splat_frames.input,
         expand(rules.split_images.output,
                sim_domain=["real","fake"],
                sigproc_domain=["real","fake"],
-               tier=["gauss"], apa=apa_iota)
-
-rule just_splat_images:
-    input:
-        rules.just_splat_frames.input,
+               tier=["gauss"], apa=apa_iota),
         expand(rules.split_splat_images.output,
                tier=["splat"], apa=apa_iota)
 
@@ -514,7 +524,6 @@ rule just_splat_images:
 rule all_images:
     input:
         rules.just_images.input,
-        rules.just_splat_images.input,
         expand(
             rules.plot_split_images.output,
             sim_domain = ["fake"],
diff --git a/cfg/ioutils.jsonnet b/cfg/ioutils.jsonnet
index 16f0a2b..43abb84 100644
--- a/cfg/ioutils.jsonnet
+++ b/cfg/ioutils.jsonnet
@@ -25,12 +25,36 @@ local ut = import 'utils.jsonnet';
         }}, nin=1, nout=1),
 
     // Use to cap off a frame stream with a sink.
-    frame_sink(name="frame-sink") :: pg.pnode({
+    frame_cap(name="frame-cap") :: pg.pnode({
         type: "DumpFrames",
         name: name,
     }, nin=1, nout=0),    
 
 
+    // Sink a frame to a tar stream.  Filename extension can be .tar,
+    // .tar.bz2 or .tar.gz.  There's no monkey business with a %d in
+    // the file name.  Pass in a unique, literal file name.  Same goes
+    // for tags.
+    frame_sink(name, outfile, tags=[], digitize=false) :: 
+        pg.pnode({
+            type: "FrameFileSink",
+            name: name,
+            data: {
+                outname: outfile,
+                tags: tags,
+                digitize: digitize,
+            },
+        }, nin=1, nout=0),
+        
+    frame_tap(name, sink, tag, cap=false) :: 
+        if cap
+        then sink
+        else pg.fan.tap('FrameFanout', sink, name,
+                        tag_rules=[ // one for each port!
+                            {frame:{'.*':tag}},
+                            {frame:{'.*':tag}},
+                        ]),
+
     // Save frames to outfile.
     //
     // name, outfile and elements of the tags list may have a single
@@ -52,7 +76,7 @@ local ut = import 'utils.jsonnet';
     frame_out(name, index, outfile, tags=["gauss%d"], digitize=false, cap=true) :: {
         local nam = if ut.haspct(name) then name%index else name,
         local tint = [if ut.haspct(t) then t%index else t for t in tags],
-        local end = if cap then [$.frame_sink(nam)] else [],
+        local end = if cap then [$.frame_cap(nam)] else [],
         local outf = if ut.haspct(outfile) then outfile%index else ut.basename_append(outfile, "-apa%d"%index),
 
         ret: pg.pipeline([$.frame_save_npz(nam, outf, digitize=digitize, tags=tint)]
diff --git a/cfg/main-depos-sigproc.jsonnet b/cfg/main-depos-sigproc.jsonnet
index 2fc5cc3..1241cac 100644
--- a/cfg/main-depos-sigproc.jsonnet
+++ b/cfg/main-depos-sigproc.jsonnet
@@ -24,15 +24,14 @@
 // not given, only signal is simulated.
 //
 // If "taps" is given it specifies a mapping from a data tier key word
-// to a file name.  The key is one of the conventional tags:
+// to a file pattern.  The key is one of the conventional tags:
 //
 // - orig :: means the ADC-level frames out of the simulation
 // - gauss :: means the signal processing with Gaussian filter
 //
-// The file name may have a "%" formatter which will be interpolated
-// against the APA ID number.  If omitted, "-apa%d" will be inserted
-// at the end of the base file name just prior to the extention
-// (likely .npz).
+// The file pattern MUST have a %d format marker which will be
+// interpolated on the APA ID.
+
 
 local wc = import "wirecell.jsonnet";
 local pg = import "pgraph.jsonnet";
@@ -72,10 +71,13 @@ function(input, taps, wires, resps_sim, resps_sigproc, noisef=null, thread='sing
                       params.daq.nticks,
                       params.daq.tick);
 
-    local tap_out(tap, apaid) =
-        if std.objectHas(taps, tap)
-        then [io.frame_out(tap+"%d", apaid, taps[tap], tags=[tap+"%d"], cap = tap=="gauss")]
-        else [];
+    local tap_out(tap, apaid, cap=false) = {
+        local name = "%s%d"%[tap,apaid],
+        local digi = tap == "raw" || tap == "orig",
+        res: if std.objectHas(taps, tap)
+             then [io.frame_tap(name, io.frame_sink(name, taps[tap]%apaid, tags=[name], digitize=digi), name, cap)]
+             else []
+    }.res;
 
     local sim(n) = [
         local anode = anodes[n];
@@ -95,7 +97,7 @@ function(input, taps, wires, resps_sim, resps_sigproc, noisef=null, thread='sing
            params.daq.nticks, params.daq.tick),
     ] + tap_out("raw", n) + [
         sp(anodes[n], robjs_sigproc.fr, robjs_sigproc.er, spfilt, adcpermv)
-    ] + tap_out("gauss", n);
+    ] + tap_out("gauss", n, true);
 
     local oneapa(n) = pg.pipeline(sim(n) + nfsp(n));
 
diff --git a/cfg/main-depos-splat.jsonnet b/cfg/main-depos-splat.jsonnet
index 5aca79f..9264ac3 100644
--- a/cfg/main-depos-splat.jsonnet
+++ b/cfg/main-depos-splat.jsonnet
@@ -22,10 +22,9 @@
 //
 // - splat :: the output of DepoSplat.
 //
-// The file name may have a "%" formatter which will be interpolated
-// against the APA ID number.  If omitted, "-apa%d" will be inserted
-// at the end of the base file name just prior to the extention
-// (likely .npz).
+// The file name must have a "%d" formatter which will be interpolated
+// against the APA ID number.  Tap files likely one of .tar, .tar.gz
+// or .tar.bz2.
 
 local wc = import "wirecell.jsonnet";
 local pg = import "pgraph.jsonnet";
@@ -54,12 +53,15 @@ function(input, taps, wires, thread='single')
 
     local drifter = tz.drifter(params.det.volumes, params.lar, random);
 
-    local tap_out(tap, apaid) =
-        if std.objectHas(taps, tap)
-        then [io.frame_out(tap+"%d", apaid, taps[tap], tags=[tap+"%d"], cap = tap=="gauss")]
-        else [];
+    local tap_out(tap, apaid, cap=true) = {
+        local name = "%s%d"%[tap,apaid],
+        local digi = tap == "raw" || tap == "orig",
+        res: if std.objectHas(taps, tap)
+             then [io.frame_tap(name, io.frame_sink(name, taps[tap]%apaid, tags=[name], digitize=digi), name, cap)]
+             else []
+    }.res;
 
-    local splat(n, ) = [
+    local splat(n) = [
         local anode = anodes[n];
         tz.splat(anode, params.daq, params.lar, random)
     ] + tap_out("splat", n);

From 535aeff83f1fa7e4a13ada8ace9c48902cf4ebab Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Thu, 19 Aug 2021 12:12:54 -0400
Subject: [PATCH 14/15] Make configurable saving orig frame

---
 Snakefile | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/Snakefile b/Snakefile
index 9d86c6a..24f2c1b 100644
--- a/Snakefile
+++ b/Snakefile
@@ -26,8 +26,16 @@ nevents = int(config.get("nevents", 10))
 depotimes = config.get("depotimes", "-3*ms,6*ms")
 wcloglvl = config.get("wcloglvl", "info")
 
-# limit number of threads per wire-cell job
+# Which intermediate data tier(s) to save from the full simulation
+# chain.  It may include "orig".  The "gauss" tier will always be included.
+frame_tap_tiers = list(config.get("frame_tap_tiers", ('orig', )))
+if "gauss" not in frame_tap_tiers:
+    frame_tap_tiers += ["gauss"]
+
+
+# limit number of threads given to a wire-cell job
 wct_threads = int(config.get("threads", 1))
+
 # single threaded uses Pgrapher, multi uses TbbFlow
 wct_threading = "single" if wct_threads == 1 else "multi"
 print(f'WCT THREADS {wct_threads} ({wct_threading})')
@@ -222,7 +230,7 @@ frames_wildcard = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-
 def frame_taps(w):
     frames_pattern = f'{datadir}/frames/{{tier}}/{{sim_domain}}-{{sigproc_domain}}-frames-apa%d.{frames_ext}'
     taps = list()
-    for tier in ('orig', 'gauss'):
+    for tier in frame_tap_tiers:
         d = dict(w)
         d["tier"] = tier
         taps.append('"%s":"%s"' % (tier, frames_pattern.format(**d)))

From 95b87a515f247e1e3b75e957a03eb2476d533021 Mon Sep 17 00:00:00 2001
From: Brett Viren 
Date: Thu, 19 Aug 2021 15:48:38 -0400
Subject: [PATCH 15/15] More cleanups and tweaks

---
 README.org   |  45 ++++++++++++++++++++++
 Snakefile    | 105 +++++++++++++++++++++++++++++++++++++--------------
 toyzero.yaml |  13 ++++---
 3 files changed, 130 insertions(+), 33 deletions(-)

diff --git a/README.org b/README.org
index 228ea67..87afbd5 100644
--- a/README.org
+++ b/README.org
@@ -573,3 +573,48 @@ made available.  If the changes are generally useful, please consider
 making a PR!
  
 
+* Production
+
+We run from containers.  Eg, as a mongo ~docker~ command that runs
+~snakemake~ in the ~toyzero~ container.
+
+#+begin_example
+
+  $ docker run \
+    --user user \
+    --volume (pwd):/data \
+    -ti ls4gan/toyzero:0.3.0 \
+    "cd toyzero && \
+     snakemake just_tar --notemp -j1 -p \
+     --config seed=1234 outdir=/data ntracks=100 nevents=10 wcloglvl=debug threads=8"
+
+#+end_example
+
+Or, one layer down in the ~wirecell~ container, assuming you have
+~toyzero~ checked out locally:
+
+#+begin_example
+
+  $ cd .. # parent holding local toyzero/
+  $ mkdir run
+  $ cd run/
+  $ cp -a ../toyzero/{Snakefile,cfg,toyzero.yaml} .
+  $ docker run \
+      --user user \
+      --volume (pwd):/data \
+      -ti ls4gan/wirecell:0.16.0 \
+      "cd /data && \
+       snakemake just_tar -j1 -p \
+       --config seed=1234 ntracks=100 nevents=10 wcloglvl=debug threads=8"
+  $ ls -l toyzero-100-10-1234.tar
+
+#+end_example
+
+Note: will likely want to set ~threads=1~ for batch and *MUST* set
+~seed=XYZ~ uniquely for each submission.  The ~outdir~ setting may be used
+if output should not go to the CWD.  The tar file base name can be
+controlled with ~outname~.  Intermediate files that eventually go in to
+the tar file land in ~{outdir}/seed-{seed}/~.  The ~./.snakemake/~
+directory receives snakemake control and log files.  If run with
+~--notemp~ then (ironically, should be named ~--yestemp~) temporary files
+marked with ~temp()~ in the Snakefile are *kept*.
diff --git a/Snakefile b/Snakefile
index 24f2c1b..790e99a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -16,9 +16,6 @@ plotdir = config.get("plotdir", "plots")
 logdir = config.get("logdir", "logs")
 outdir = config.get("outdir", os.environ.get("TOYZERO_OUTDIR", "."))
 
-datadir = os.path.abspath(os.path.join(outdir, datadir))
-plotdir = os.path.abspath(os.path.join(outdir, plotdir))
-logdir  = os.path.abspath(os.path.join(outdir, logdir))
     
 seed = config.get("seed", "1,2,3,4")
 ntracks = int(config.get("ntracks", 10))
@@ -26,6 +23,15 @@ nevents = int(config.get("nevents", 10))
 depotimes = config.get("depotimes", "-3*ms,6*ms")
 wcloglvl = config.get("wcloglvl", "info")
 
+seedlst_ = str(seed).replace(",","-")
+seeddir = f'seed-{seedlst_}'
+outuniq = os.path.abspath(os.path.join(outdir, seeddir))
+datadir = os.path.abspath(os.path.join(outuniq, datadir))
+plotdir = os.path.abspath(os.path.join(outuniq, plotdir))
+logdir  = os.path.abspath(os.path.join(outuniq, logdir))
+
+outname = config.get("outname", f'{outdir}/toyzero-{ntracks}-{nevents}-{seed}')
+
 # Which intermediate data tier(s) to save from the full simulation
 # chain.  It may include "orig".  The "gauss" tier will always be included.
 frame_tap_tiers = list(config.get("frame_tap_tiers", ('orig', )))
@@ -38,7 +44,7 @@ wct_threads = int(config.get("threads", 1))
 
 # single threaded uses Pgrapher, multi uses TbbFlow
 wct_threading = "single" if wct_threads == 1 else "multi"
-print(f'WCT THREADS {wct_threads} ({wct_threading})')
+# print(f'WCT THREADS {wct_threads} ({wct_threading})')
 
 # The rest are hard wired for now
 wcdata_url = "https://github.com/WireCell/wire-cell-data/raw/master"
@@ -112,10 +118,14 @@ rule plot_resp:
     wirecell-sigproc plot-response {input} {output}
     '''
 
-rule all_resp:
+rule just_resp:
     input:
         rules.get_resp_real.output,
         rules.gen_resp_fake.output,
+
+rule all_resp:
+    input:
+        rules.just_resp.input,
         expand(rules.plot_resp.output, domain=["real","fake"])
 
 # wires - get wires file
@@ -140,9 +150,13 @@ rule plot_wires:
     wirecell-util plot-wires {input} {output}
     '''
 
-rule all_wires:
+rule just_wires:
     input:
         rules.get_wires.output,
+
+rule all_wires:
+    input:
+        rules.just_wires.input,
         rules.plot_wires.output
 
 
@@ -174,9 +188,14 @@ rule plot_depos:
     wirecell-gen plot-sim {input} {output} -p depo
     '''
         
+rule just_depos:
+    input:
+        expand(rules.gen_depos.output, wire=wires)
+
+
 rule all_depos:
     input:
-        expand(rules.gen_depos.output, wire=wires),
+        rules.just_depos.input,
         expand(rules.plot_depos.output, wire=wires)
 
 
@@ -254,6 +273,8 @@ rule sim_frames:
         temp(sim_frame_files())
     params:
         taps = frame_taps
+    log:
+        f'{logdir}/sim-frames-{{sim_domain}}-{{sigproc_domain}}.log'
     benchmark:
         f'{logdir}/sim-frames-{{sim_domain}}-{{sigproc_domain}}.tsv'
     shell: '''
@@ -261,7 +282,7 @@ rule sim_frames:
     wire-cell \
     --threads {wct_threads} \
     -A thread={wct_threading} \
-    -l stdout -L {config[wcloglvl]} \
+    -l {log} -L {config[wcloglvl]} \
     -P cfg \
     -A input={input.depos} \
     --tla-code 'taps={params.taps}' \
@@ -283,12 +304,16 @@ rule splat_frames:
         temp([f'{datadir}/frames/splat/splat-frames-apa{apa}.{frames_ext}' for apa in apa_iota])
     params:
         taps = f'{{"splat":"{datadir}/frames/splat/splat-frames-apa%d.{frames_ext}"}}'
+    log:
+        f'{logdir}/splat-frames.log'
+    benchmark:
+        f'{logdir}/splat-frames.tsv'
     shell: '''
     rm -f {output}; 
     wire-cell \
     --threads {wct_threads} \
     -A thread={wct_threading} \
-    -l stdout -L {config[wcloglvl]} \
+    -l {log} -L {config[wcloglvl]} \
     -P cfg \
     -A input={input.depos} \
     --tla-code 'taps={params.taps}' \
@@ -337,9 +362,13 @@ rule all_splat_frames:
 rule just_frames:
     input:
         expand(rules.sim_frames.output,
-               sim_domain=["real","fake"],
-               sigproc_domain=["real","fake"],
+               sim_domain=["real"],
+               sigproc_domain=["fake"],
                ),
+        expand(rules.sim_frames.output,
+               sim_domain=["fake"],
+               sigproc_domain=["fake"],
+               )
         
 
 rule all_frames:
@@ -520,11 +549,18 @@ rule plot_split_splat_images:
 rule just_images:
     input:
         rules.just_frames.input,
-        rules.just_splat_frames.input,
         expand(rules.split_images.output,
-               sim_domain=["real","fake"],
-               sigproc_domain=["real","fake"],
+               sim_domain=["real"],
+               sigproc_domain=["fake"],
                tier=["gauss"], apa=apa_iota),
+        expand(rules.split_images.output,
+               sim_domain=["fake"],
+               sigproc_domain=["fake"],
+               tier=["gauss"], apa=apa_iota)
+
+rule just_splat_images:
+    input:
+        rules.just_splat_frames.input,
         expand(rules.split_splat_images.output,
                tier=["splat"], apa=apa_iota)
 
@@ -536,32 +572,26 @@ rule all_images:
             rules.plot_split_images.output,
             sim_domain = ["fake"],
             sigproc_domain = ["fake"],
-            tier = ["orig"],
+            tier = ["gauss"],
             event  = [0], apa=apa_iota, plane=["U","V","W"],
             ext    = ["png"],
-            cmap   = ["seismic"],
+            cmap   = ["viridis"],
             zoomlevel=[1, 2],
         ),
         expand(
             rules.plot_split_images.output,
             sim_domain = ["real"],
-            sigproc_domain = ["real"],
-            tier = ["orig"],
-            event  = [0], apa=apa_iota, plane=["U","V","W"],
-            ext    = ["png"],
-            cmap   = ["seismic"],
-            zoomlevel=[1, 2],
-        ),
-        expand(
-            rules.plot_split_images.output,
-            sim_domain = ["real","fake"],
-            sigproc_domain = ["real","fake"],
+            sigproc_domain = ["fake"],
             tier = ["gauss"],
             event  = [0], apa=apa_iota, plane=["U","V","W"],
             ext    = ["png"],
             cmap   = ["viridis"],
             zoomlevel=[1, 2],
-        ),
+        )
+
+rule all_splat:
+    input:
+        rules.just_splat_images.input,
         expand(
             rules.plot_split_splat_images.output,
             tier = ["splat"],
@@ -572,6 +602,11 @@ rule all_images:
         )
 
 
+rule just:
+    input:
+        rules.just_frames.input,
+        rules.just_images.input
+
 rule all:
     input:
         rules.all_resp.input,
@@ -580,3 +615,17 @@ rule all:
         rules.all_frames.input,
         rules.all_images.input
 
+rule just_tar:
+    input:
+        rules.just.input,
+    output:
+        f'{outname}.tar'
+    shell: '''
+    tar --exclude data/depos \
+        --exclude data/noise \
+        --exclude data/wires \
+        --exclude data/resps \
+        --exclude data/frames/orig \
+        -cf {output} {outuniq}
+    '''
+
diff --git a/toyzero.yaml b/toyzero.yaml
index 761206a..6da7d11 100644
--- a/toyzero.yaml
+++ b/toyzero.yaml
@@ -3,11 +3,14 @@
 # This is the default toyzero config file.
 # Use like:
 #   snakemake --configfile mycfg.yaml -jall all
+# Or further, like
+#   snakemake --configfile mycfg.yaml -jall all --config outdir=other
+# See top of snakefile for what can be set here.
 outdir: "."
-datadir: "data"
-plotdir: "plots"
+# best to set something unique on the CLI!!!
+# seed will be used as an intermediate under outdir
 seed: "1,2,3,4"
 ntracks: 10
-nevents: 10
-# how noisy wire-cell should be.  "debug" is more, "error" is less
-wcloglvl: info
+nevents: 1
+# how noisy wire-cell should be.  "debug" is more, "info" is less
+wcloglvl: debug